From 66f6b06f173578177d83458473e6f38d62ffb69e Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Mon, 3 Jul 2023 16:35:10 +0200 Subject: [PATCH 001/101] [pmx_biobb] update 4.1.2 build 1: Python 3.7 (#41809) * [pmx_biobb] update 4.1.2 build 1: Python 3.7 * Update meta.yaml * Update meta.yaml --- recipes/pmx_biobb/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pmx_biobb/meta.yaml b/recipes/pmx_biobb/meta.yaml index 8746c50713770..ae99187bd9df6 100644 --- a/recipes/pmx_biobb/meta.yaml +++ b/recipes/pmx_biobb/meta.yaml @@ -13,7 +13,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" @@ -24,13 +24,13 @@ requirements: - {{ compiler('fortran') }} - make host: - - python >=3.7 + - python =3.7 - setuptools - scipy - matplotlib-base - rdkit run: - - python >=3.7 + - python =3.7 - scipy - matplotlib-base - rdkit From b6771bc135571babf14e4285e4663b29ca47ca84 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 3 Jul 2023 15:18:50 -0600 Subject: [PATCH 002/101] Update r-cellosaurus to 0.5.4 (#41817) --- recipes/r-cellosaurus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-cellosaurus/meta.yaml b/recipes/r-cellosaurus/meta.yaml index ab8fc879721c5..a04d61cd0b7a7 100644 --- a/recipes/r-cellosaurus/meta.yaml +++ b/recipes/r-cellosaurus/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.3" %} +{% set version = "0.5.4" %} {% set github = "https://github.com/acidgenomics/r-cellosaurus" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 1b46d192c9abf1c0668d30625b8fefa0046a8a5ff1baa3ba01fe90f11fb5f562 + sha256: 51a2895971a70e6d4eddf1db40e0d1641ac7a9c88036b8c34171014241e1fda2 build: noarch: generic From 82325d9207a7c290a09ab498c3feba2a433cb9c4 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Tue, 4 Jul 2023 06:46:05 +0200 Subject: [PATCH 003/101] [pmx_biobb] update 4.1.2 build 2: Python [no vers] (#41812) --- recipes/pmx_biobb/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pmx_biobb/meta.yaml b/recipes/pmx_biobb/meta.yaml index ae99187bd9df6..c711e8d8d62ec 100644 --- a/recipes/pmx_biobb/meta.yaml +++ b/recipes/pmx_biobb/meta.yaml @@ -13,7 +13,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 1 + number: 2 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" @@ -24,13 +24,13 @@ requirements: - {{ compiler('fortran') }} - make host: - - python =3.7 + - python - setuptools - scipy - matplotlib-base - rdkit run: - - python =3.7 + - python - scipy - matplotlib-base - rdkit From defb45d4dc7e6154460af5bd56001397763551ec Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Tue, 4 Jul 2023 09:23:42 +0200 Subject: [PATCH 004/101] Update MoDLE to v1.1.0 (#41060) * Bump version * Add integration tests * test.sh -> run_test.sh * Bugfix * Bugfix * Bugfix * Debugging * Debugging * Bugfix * Try to manually specify conan profiles * Simplify a bit * Fix typos * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Let's try to simplify things... * Linux CI is working fine: let's skip it for now * Try to see if this compilation error only affects boost * The problem seems to be only with boost. Let's focus on that * Try to build boost and its deps in two stages * Bugfix * debugging compilation issues on macOS is fun... * Bugfix * Try to bump boost * Build b2 * Debugging * Debugging * Debugging * Update url * Update url * Lucky me, a compiler segfault... * Debug test failure * Remove unnecessary files * Fix sed on MacOS * Install shasum* * Update URL --------- Co-authored-by: Devon Ryan --- recipes/modle/build.sh | 19 ++-- recipes/modle/build_failure.linux-64.yaml | 104 ---------------------- recipes/modle/build_failure.osx-64.yaml | 104 ---------------------- recipes/modle/conan_profiles/clang | 9 ++ recipes/modle/conan_profiles/gcc | 8 ++ recipes/modle/cross-linux.cmake | 1 + recipes/modle/meta.yaml | 21 ++++- recipes/modle/run_test.sh | 24 +++++ 8 files changed, 71 insertions(+), 219 deletions(-) delete mode 100644 recipes/modle/build_failure.linux-64.yaml delete mode 100644 recipes/modle/build_failure.osx-64.yaml create mode 100644 recipes/modle/conan_profiles/clang create mode 100644 recipes/modle/conan_profiles/gcc create mode 100755 recipes/modle/run_test.sh diff --git a/recipes/modle/build.sh b/recipes/modle/build.sh index 48989353034b5..af31fd2fb2785 100755 --- a/recipes/modle/build.sh +++ b/recipes/modle/build.sh @@ -17,15 +17,17 @@ export CONAN_HOME="$scratch/conan" # shellcheck disable=SC2064 trap "rm -rf '$scratch'" EXIT +# Conan doesn't detect compiler name and version when using cc/c++ +TMPBIN="$scratch/bin" +mkdir "$TMPBIN" + declare -a CMAKE_PLATFORM_FLAGS if [[ ${HOST} =~ .*darwin.* ]]; then export MACOSX_DEPLOYMENT_TARGET=10.15 # Required to use std::filesystem CMAKE_PLATFORM_FLAGS+=(-DCMAKE_OSX_SYSROOT="${CONDA_BUILD_SYSROOT}") + conan_profile='clang' else CMAKE_PLATFORM_FLAGS+=(-DCMAKE_TOOLCHAIN_FILE="${RECIPE_DIR}/cross-linux.cmake") - # Conan doesn't detect compiler name and version when using cc/c++ - TMPBIN="$scratch/bin" - mkdir "$TMPBIN" ln -sf "$CC" "$TMPBIN/gcc" ln -sf "$CXX" "$TMPBIN/g++" @@ -33,15 +35,18 @@ else export PATH="$TMPBIN:$PATH" export CC="$TMPBIN/gcc" export CXX="$TMPBIN/g++" + conan_profile='gcc' fi -conan profile detect +# Remember to update these profiles when bioconda's compiler toolchains are updated +mkdir -p "$CONAN_HOME/profiles/" +ln -s "${RECIPE_DIR}/conan_profiles/$conan_profile" "$CONAN_HOME/profiles/$conan_profile" -# Build everything from source to avoid ABI issues due to old GLIBC/GLIBCXX conan install conanfile.txt \ --build="*" \ - -s build_type=Release \ - -s compiler.cppstd=17 \ + --build="b2/*" \ + -pr:b "$conan_profile" \ + -pr:h "$conan_profile" \ --output-folder=build/ # Add bioconda suffix to MoDLE version diff --git a/recipes/modle/build_failure.linux-64.yaml b/recipes/modle/build_failure.linux-64.yaml deleted file mode 100644 index aea7250a1291e..0000000000000 --- a/recipes/modle/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 251bacb41264d22c9c003d1390440d9f4ca356b10623ac2fbc0802978e083d6d # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - bshoshany-thread-pool/3.3.0:[0m Checking remote: conancenter[0m - bshoshany-thread-pool/3.3.0:[0m Downloaded recipe revision 22e99aee6babc19e679754d95dad2de4[0m - catch2/3.3.2:[0m Not found in local cache, looking in remotes...[0m - catch2/3.3.2:[0m Checking remote: conancenter[0m - catch2/3.3.2:[0m Downloaded recipe revision be6a2f0225146ba4fd8573ee9013e5ae[0m - cli11/2.3.2:[0m Not found in local cache, looking in remotes...[0m - cli11/2.3.2:[0m Checking remote: conancenter[0m - cli11/2.3.2:[0m Downloaded recipe revision 8ccdf14fb1ad53532d498c16ae580b4b[0m - concurrentqueue/1.0.3:[0m Not found in local cache, looking in remotes...[0m - concurrentqueue/1.0.3:[0m Checking remote: conancenter[0m - concurrentqueue/1.0.3:[0m Downloaded recipe revision c1cb7d960d8b64073643b45fa63f0bd1[0m - cpp-sort/1.14.0:[0m Not found in local cache, looking in remotes...[0m - cpp-sort/1.14.0:[0m Checking remote: conancenter[0m - cpp-sort/1.14.0:[0m Downloaded recipe revision 3453aaaf83c1dae4214ca3b5c4c3a5c8[0m - fast_float/4.0.0:[0m Not found in local cache, looking in remotes...[0m - fast_float/4.0.0:[0m Checking remote: conancenter[0m - fast_float/4.0.0:[0m Downloaded recipe revision 90cac63d3ae321f6318b9abf8af9cbb1[0m - fmt/9.1.0:[0m Not found in local cache, looking in remotes...[0m - fmt/9.1.0:[0m Checking remote: conancenter[0m - fmt/9.1.0:[0m Downloaded recipe revision e747928f85b03f48aaf227ff897d9634[0m - hdf5/1.14.0:[0m Not found in local cache, looking in remotes...[0m - hdf5/1.14.0:[0m Checking remote: conancenter[0m - hdf5/1.14.0:[0m Downloaded recipe revision 011206975dc4c5ca80dd612d3a34cab3[0m - cmake/3.26.4:[0m Not found in local cache, looking in remotes...[0m - cmake/3.26.4:[0m Checking remote: conancenter[0m - cmake/3.26.4:[0m Downloaded recipe revision 0b40747e190e755932767f2ec4768ff5[0m - highfive/2.7.1:[0m Not found in local cache, looking in remotes...[0m - highfive/2.7.1:[0m Checking remote: conancenter[0m - highfive/2.7.1:[0m Downloaded recipe revision a73bc6937c9add30c9d47a7a70a466eb[0m - libarchive/3.6.2:[0m Not found in local cache, looking in remotes...[0m - libarchive/3.6.2:[0m Checking remote: conancenter[0m - libarchive/3.6.2:[0m Downloaded recipe revision b768ab8c0dcfb9e27b912a7f32fd02c1[0m - libiconv/1.17:[0m Not found in local cache, looking in remotes...[0m - libiconv/1.17:[0m Checking remote: conancenter[0m - libiconv/1.17:[0m Downloaded recipe revision fa54397801cd96911a8294bc5fc76335[0m - lz4/1.9.4:[0m Not found in local cache, looking in remotes...[0m - lz4/1.9.4:[0m Checking remote: conancenter[0m - lz4/1.9.4:[0m Downloaded recipe revision bce1f314775b83c195dffc8e177ff368[0m - lzo/2.10:[0m Not found in local cache, looking in remotes...[0m - lzo/2.10:[0m Checking remote: conancenter[0m - lzo/2.10:[0m Downloaded recipe revision 5725914235423c771cb1c6b607109b45[0m - libbigwig/0.4.7:[0m Not found in local cache, looking in remotes...[0m - libbigwig/0.4.7:[0m Checking remote: conancenter[0m - libbigwig/0.4.7:[0m Downloaded recipe revision 97113380bd925b2220b1d1e63c454d91[0m - zlib-ng/2.0.7:[0m Not found in local cache, looking in remotes...[0m - zlib-ng/2.0.7:[0m Checking remote: conancenter[0m - zlib-ng/2.0.7:[0m Downloaded recipe revision fbf3d453595da4be4245283c4ca065b8[0m - libcuckoo/0.3.1:[0m Not found in local cache, looking in remotes...[0m - libcuckoo/0.3.1:[0m Checking remote: conancenter[0m - libcuckoo/0.3.1:[0m Downloaded recipe revision 7e514d4c23a9aba3d8d80758824e9dc0[0m - [1m[33mGraph root[0m - [1m[36m conanfile.txt: /opt/conda/conda-bld/modle_1686044039950/work/conanfile.txt[0m - [1m[33mRequirements[0m - [1m[36m abseil/20230125.3#5431a4c609f5fb48bb8d8567e953243f - Downloaded (conancenter)[0m - [1m[36m bitflags/1.5.0#626da9d1913161321841f30caf9b994e - Downloaded (conancenter)[0m - [1m[36m boost/1.81.0#9bd7ae86a881631b6cc76590621e470b - Downloaded (conancenter)[0m - [1m[36m bshoshany-thread-pool/3.3.0#22e99aee6babc19e679754d95dad2de4 - Downloaded (conancenter)[0m - [1m[36m bzip2/1.0.8#411fc05e80d47a89045edc1ee6f23c1d - Downloaded (conancenter)[0m - [1m[36m catch2/3.3.2#be6a2f0225146ba4fd8573ee9013e5ae - Downloaded (conancenter)[0m - [1m[36m cli11/2.3.2#8ccdf14fb1ad53532d498c16ae580b4b - Downloaded (conancenter)[0m - [1m[36m concurrentqueue/1.0.3#c1cb7d960d8b64073643b45fa63f0bd1 - Downloaded (conancenter)[0m - [1m[36m cpp-sort/1.14.0#3453aaaf83c1dae4214ca3b5c4c3a5c8 - Downloaded (conancenter)[0m - [1m[36m fast_float/4.0.0#90cac63d3ae321f6318b9abf8af9cbb1 - Downloaded (conancenter)[0m - [1m[36m fmt/9.1.0#e747928f85b03f48aaf227ff897d9634 - Downloaded (conancenter)[0m - [1m[36m hdf5/1.14.0#011206975dc4c5ca80dd612d3a34cab3 - Downloaded (conancenter)[0m - [1m[36m highfive/2.7.1#a73bc6937c9add30c9d47a7a70a466eb - Downloaded (conancenter)[0m - [1m[36m libarchive/3.6.2#b768ab8c0dcfb9e27b912a7f32fd02c1 - Downloaded (conancenter)[0m - [1m[36m libbigwig/0.4.7#97113380bd925b2220b1d1e63c454d91 - Downloaded (conancenter)[0m - [1m[36m libcuckoo/0.3.1#7e514d4c23a9aba3d8d80758824e9dc0 - Downloaded (conancenter)[0m - [1m[36m libiconv/1.17#fa54397801cd96911a8294bc5fc76335 - Downloaded (conancenter)[0m - [1m[36m lz4/1.9.4#bce1f314775b83c195dffc8e177ff368 - Downloaded (conancenter)[0m - [1m[36m lzo/2.10#5725914235423c771cb1c6b607109b45 - Downloaded (conancenter)[0m - [1m[36m xz_utils/5.4.2#b6ee8320403def553418874435445982 - Downloaded (conancenter)[0m - [1m[36m zlib/1.2.13#e377bee636333ae348d51ca90874e353 - Downloaded (conancenter)[0m - [1m[36m zlib-ng/2.0.7#fbf3d453595da4be4245283c4ca065b8 - Downloaded (conancenter)[0m - [1m[36m zstd/1.5.5#93372fe14bb7883bd4de82914e0a1841 - Downloaded (conancenter)[0m - [1m[33mBuild requirements[0m - [1m[36m b2/4.9.6#2e02945ad41739b8051247d14fe8297d - Downloaded (conancenter)[0m - [1m[36m cmake/3.26.4#0b40747e190e755932767f2ec4768ff5 - Downloaded (conancenter)[0m - [1m[33mResolved version ranges[0m - [1m[36m cmake/[>=3.18 <4]: cmake/3.26.4[0m - [31mERROR: Version conflict: None->lzo/2.10, None->lzo/2.10.[0m - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/modle_1686044039950/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/modle/build_failure.osx-64.yaml b/recipes/modle/build_failure.osx-64.yaml deleted file mode 100644 index d2c99f037b8fe..0000000000000 --- a/recipes/modle/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 251bacb41264d22c9c003d1390440d9f4ca356b10623ac2fbc0802978e083d6d # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - bshoshany-thread-pool/3.3.0: Checking remote: conancenter - bshoshany-thread-pool/3.3.0: Downloaded recipe revision 22e99aee6babc19e679754d95dad2de4 - catch2/3.3.2: Not found in local cache, looking in remotes... - catch2/3.3.2: Checking remote: conancenter - catch2/3.3.2: Downloaded recipe revision be6a2f0225146ba4fd8573ee9013e5ae - cli11/2.3.2: Not found in local cache, looking in remotes... - cli11/2.3.2: Checking remote: conancenter - cli11/2.3.2: Downloaded recipe revision 8ccdf14fb1ad53532d498c16ae580b4b - concurrentqueue/1.0.3: Not found in local cache, looking in remotes... - concurrentqueue/1.0.3: Checking remote: conancenter - concurrentqueue/1.0.3: Downloaded recipe revision c1cb7d960d8b64073643b45fa63f0bd1 - cpp-sort/1.14.0: Not found in local cache, looking in remotes... - cpp-sort/1.14.0: Checking remote: conancenter - cpp-sort/1.14.0: Downloaded recipe revision 3453aaaf83c1dae4214ca3b5c4c3a5c8 - fast_float/4.0.0: Not found in local cache, looking in remotes... - fast_float/4.0.0: Checking remote: conancenter - fast_float/4.0.0: Downloaded recipe revision 90cac63d3ae321f6318b9abf8af9cbb1 - fmt/9.1.0: Not found in local cache, looking in remotes... - fmt/9.1.0: Checking remote: conancenter - fmt/9.1.0: Downloaded recipe revision e747928f85b03f48aaf227ff897d9634 - hdf5/1.14.0: Not found in local cache, looking in remotes... - hdf5/1.14.0: Checking remote: conancenter - hdf5/1.14.0: Downloaded recipe revision 011206975dc4c5ca80dd612d3a34cab3 - cmake/3.26.4: Not found in local cache, looking in remotes... - cmake/3.26.4: Checking remote: conancenter - cmake/3.26.4: Downloaded recipe revision 0b40747e190e755932767f2ec4768ff5 - highfive/2.7.1: Not found in local cache, looking in remotes... - highfive/2.7.1: Checking remote: conancenter - highfive/2.7.1: Downloaded recipe revision a73bc6937c9add30c9d47a7a70a466eb - libarchive/3.6.2: Not found in local cache, looking in remotes... - libarchive/3.6.2: Checking remote: conancenter - libarchive/3.6.2: Downloaded recipe revision b768ab8c0dcfb9e27b912a7f32fd02c1 - libiconv/1.17: Not found in local cache, looking in remotes... - libiconv/1.17: Checking remote: conancenter - libiconv/1.17: Downloaded recipe revision fa54397801cd96911a8294bc5fc76335 - lz4/1.9.4: Not found in local cache, looking in remotes... - lz4/1.9.4: Checking remote: conancenter - lz4/1.9.4: Downloaded recipe revision bce1f314775b83c195dffc8e177ff368 - lzo/2.10: Not found in local cache, looking in remotes... - lzo/2.10: Checking remote: conancenter - lzo/2.10: Downloaded recipe revision 5725914235423c771cb1c6b607109b45 - libbigwig/0.4.7: Not found in local cache, looking in remotes... - libbigwig/0.4.7: Checking remote: conancenter - libbigwig/0.4.7: Downloaded recipe revision 97113380bd925b2220b1d1e63c454d91 - zlib-ng/2.0.7: Not found in local cache, looking in remotes... - zlib-ng/2.0.7: Checking remote: conancenter - zlib-ng/2.0.7: Downloaded recipe revision fbf3d453595da4be4245283c4ca065b8 - libcuckoo/0.3.1: Not found in local cache, looking in remotes... - libcuckoo/0.3.1: Checking remote: conancenter - libcuckoo/0.3.1: Downloaded recipe revision 7e514d4c23a9aba3d8d80758824e9dc0 - Graph root - conanfile.txt: /opt/mambaforge/envs/bioconda/conda-bld/modle_1686044682356/work/conanfile.txt - Requirements - abseil/20230125.3#5431a4c609f5fb48bb8d8567e953243f - Downloaded (conancenter) - bitflags/1.5.0#626da9d1913161321841f30caf9b994e - Downloaded (conancenter) - boost/1.81.0#9bd7ae86a881631b6cc76590621e470b - Downloaded (conancenter) - bshoshany-thread-pool/3.3.0#22e99aee6babc19e679754d95dad2de4 - Downloaded (conancenter) - bzip2/1.0.8#411fc05e80d47a89045edc1ee6f23c1d - Downloaded (conancenter) - catch2/3.3.2#be6a2f0225146ba4fd8573ee9013e5ae - Downloaded (conancenter) - cli11/2.3.2#8ccdf14fb1ad53532d498c16ae580b4b - Downloaded (conancenter) - concurrentqueue/1.0.3#c1cb7d960d8b64073643b45fa63f0bd1 - Downloaded (conancenter) - cpp-sort/1.14.0#3453aaaf83c1dae4214ca3b5c4c3a5c8 - Downloaded (conancenter) - fast_float/4.0.0#90cac63d3ae321f6318b9abf8af9cbb1 - Downloaded (conancenter) - fmt/9.1.0#e747928f85b03f48aaf227ff897d9634 - Downloaded (conancenter) - hdf5/1.14.0#011206975dc4c5ca80dd612d3a34cab3 - Downloaded (conancenter) - highfive/2.7.1#a73bc6937c9add30c9d47a7a70a466eb - Downloaded (conancenter) - libarchive/3.6.2#b768ab8c0dcfb9e27b912a7f32fd02c1 - Downloaded (conancenter) - libbigwig/0.4.7#97113380bd925b2220b1d1e63c454d91 - Downloaded (conancenter) - libcuckoo/0.3.1#7e514d4c23a9aba3d8d80758824e9dc0 - Downloaded (conancenter) - libiconv/1.17#fa54397801cd96911a8294bc5fc76335 - Downloaded (conancenter) - lz4/1.9.4#bce1f314775b83c195dffc8e177ff368 - Downloaded (conancenter) - lzo/2.10#5725914235423c771cb1c6b607109b45 - Downloaded (conancenter) - xz_utils/5.4.2#b6ee8320403def553418874435445982 - Downloaded (conancenter) - zlib/1.2.13#e377bee636333ae348d51ca90874e353 - Downloaded (conancenter) - zlib-ng/2.0.7#fbf3d453595da4be4245283c4ca065b8 - Downloaded (conancenter) - zstd/1.5.5#93372fe14bb7883bd4de82914e0a1841 - Downloaded (conancenter) - Build requirements - b2/4.9.6#2e02945ad41739b8051247d14fe8297d - Downloaded (conancenter) - cmake/3.26.4#0b40747e190e755932767f2ec4768ff5 - Downloaded (conancenter) - Resolved version ranges - cmake/[>=3.18 <4]: cmake/3.26.4 - ERROR: Version conflict: None->lzo/2.10, None->lzo/2.10. - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/modle_1686044682356/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/modle/conan_profiles/clang b/recipes/modle/conan_profiles/clang new file mode 100644 index 0000000000000..efb06428a92bc --- /dev/null +++ b/recipes/modle/conan_profiles/clang @@ -0,0 +1,9 @@ +[settings] +arch=x86_64 +build_type=Release +compiler=clang +compiler.cppstd=17 +compiler.libcxx=libc++ +compiler.version=14 +os=Macos +os.version="10.15" diff --git a/recipes/modle/conan_profiles/gcc b/recipes/modle/conan_profiles/gcc new file mode 100644 index 0000000000000..ef7e2f6219ff1 --- /dev/null +++ b/recipes/modle/conan_profiles/gcc @@ -0,0 +1,8 @@ +[settings] +arch=x86_64 +build_type=Release +compiler=gcc +compiler.cppstd=17 +compiler.libcxx=libstdc++11 +compiler.version=13 +os=Linux diff --git a/recipes/modle/cross-linux.cmake b/recipes/modle/cross-linux.cmake index bb837eea5ba7b..b8f90c3409b9d 100644 --- a/recipes/modle/cross-linux.cmake +++ b/recipes/modle/cross-linux.cmake @@ -6,6 +6,7 @@ set(CMAKE_SYSTEM_VERSION 1) # specify the cross compiler set(CMAKE_C_COMPILER $ENV{CC}) +set(CMAKE_CXX_COMPILER $ENV{CXX}) # where is the target environment set(CMAKE_FIND_ROOT_PATH $ENV{PREFIX} $ENV{BUILD_PREFIX}/$ENV{HOST}/sysroot) diff --git a/recipes/modle/meta.yaml b/recipes/modle/meta.yaml index 40f78ad373145..602ba4b530f81 100644 --- a/recipes/modle/meta.yaml +++ b/recipes/modle/meta.yaml @@ -1,13 +1,13 @@ {% set name = "MoDLE" %} -{% set version = "1.0.1" %} -{% set sha256 = "66135d77127abac89fae1309346decd179a96ba512ded58dbdc3a8c802ca87f7" %} +{% set version = "1.1.0" %} +{% set sha256 = "f1bfd2c98ff131d555bc1504fab5c86f35521e51da87d5f66435c145e11a26e3" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 1 + number: 0 source: url: https://github.com/paulsengroup/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz @@ -17,7 +17,7 @@ requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} - - cmake >=3.20 + - cmake >=3.25 - conan >=2.0 - git >2.7 - make @@ -31,6 +31,19 @@ about: doc_url: https://github.com/paulsengroup/{{ name }}#readme test: + requires: + - cooler>=0.9 + - curl + - perl-digest-sha1 + - pyBigWig>=0.3.22 + - xz + source_files: + - cmake/FetchTestDataset.cmake + - test/scripts/compare_bwigs.py + - test/scripts/modle_integration_test.sh + - test/scripts/modle_tools_annotate_barriers_integration_test.sh + - test/scripts/modle_tools_eval_integration_test.sh + - test/scripts/modle_tools_transform_integration_test.sh commands: - modle --help - modle_tools --help diff --git a/recipes/modle/run_test.sh b/recipes/modle/run_test.sh new file mode 100755 index 0000000000000..9c188aa3242f4 --- /dev/null +++ b/recipes/modle/run_test.sh @@ -0,0 +1,24 @@ +#!/bin/bash + +set -e +set -u +set -x +set -o pipefail + +# Extract test dataset URL and checksum +url="$(grep -F 'DOWNLOAD' 'cmake/FetchTestDataset.cmake' | sed -E 's/.*DOWNLOAD[[:space:]]+//')" +checksum="$(grep -F 'EXPECTED_HASH' 'cmake/FetchTestDataset.cmake' | sed 's/.*SHA512=//')" + +# Download and extract test datasets +curl -L "$url" -o modle_test_dataset.tar.xz +echo "$checksum modle_test_dataset.tar.xz" > checksum.sha512 +shasum -c checksum.sha512 + +tar -xf modle_test_dataset.tar.xz test/data/integration_tests/ + +# Run integration tests +test/scripts/modle_integration_test.sh "$(which modle)" + +test/scripts/modle_tools_annotate_barriers_integration_test.sh "$(which modle_tools)" +test/scripts/modle_tools_eval_integration_test.sh "$(which modle_tools)" +test/scripts/modle_tools_transform_integration_test.sh "$(which modle_tools)" From 0a4ce74098625614dc025d29961adf2886cba318 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Tue, 4 Jul 2023 09:59:14 +0200 Subject: [PATCH 005/101] Scirpy: unpin pandas (#41821) v0.13 is compatible with pandas 2.0. Forgot to remove the constraints during autobump. Fixes https://github.com/scverse/scirpy/issues/426 --- recipes/scirpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/scirpy/meta.yaml b/recipes/scirpy/meta.yaml index a925157bea8ff..0304c3f000540 100644 --- a/recipes/scirpy/meta.yaml +++ b/recipes/scirpy/meta.yaml @@ -11,7 +11,7 @@ source: folder: "{{ name }}-{{ version }}" build: - number: 0 + number: 1 noarch: python script: - cd "{{ name }}-{{ version }}" @@ -29,7 +29,7 @@ requirements: - awkward >=2.1.0 - mudata >=0.2.3 - scanpy >=1.9.3 - - pandas >=1.5,<2 + - pandas >=1.5 - numpy >=1.17.0 - scipy - parasail-python From dd5adee4ce14be385b5ed726622a6965137f7ec9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 4 Jul 2023 02:31:45 -0600 Subject: [PATCH 006/101] Update treeswift to 1.1.37 (#41814) * Update treeswift to 1.1.36 * Update treeswift to 1.1.37 --- recipes/treeswift/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/treeswift/meta.yaml b/recipes/treeswift/meta.yaml index a7e9f6c83b348..29ddb697dd74e 100644 --- a/recipes/treeswift/meta.yaml +++ b/recipes/treeswift/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.35" %} +{% set version = "1.1.37" %} package: name: "treeswift" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/t/treeswift/treeswift-{{ version }}.tar.gz - sha256: cbe615f48681146adc643ead9ca4bbf1b3d65aeedb0aa6d0495086cf316d3668 + sha256: d7899104428cbb157027099fbe2fbaec1e87870ae48d561a6075a29498827b6b build: noarch: python From 0d9160a27e3d08502ed3c0d0e59f19aded4cc8a5 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Tue, 4 Jul 2023 13:20:52 +0200 Subject: [PATCH 007/101] Equivalent to #40459 (#41823) Co-authored-by: Devon Ryan --- recipes/dropest/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/dropest/meta.yaml b/recipes/dropest/meta.yaml index 1b1fe9b12cdab..281e7c2d09ed4 100644 --- a/recipes/dropest/meta.yaml +++ b/recipes/dropest/meta.yaml @@ -12,7 +12,7 @@ source: - patch build: - number: 6 + number: 7 skip: True # [osx] rpaths: - lib/R/lib/ @@ -23,11 +23,11 @@ requirements: - make - {{ compiler('cxx') }} - cmake - - bamtools host: - r-base - boost - boost-cpp + - bamtools - zlib - bzip2 - r-rcpp @@ -43,6 +43,7 @@ requirements: run: - r-base - boost + - bamtools - zlib - bzip2 - r-rcpp @@ -58,6 +59,7 @@ requirements: test: commands: + - dropest --help - droptag --help - R -e "library('dropestr')" From c8cbbb3ce2d640dd7b8466a22dcc6257cf049dda Mon Sep 17 00:00:00 2001 From: vered kunik <40732104+VeredKunik@users.noreply.github.com> Date: Tue, 4 Jul 2023 15:37:30 +0300 Subject: [PATCH 008/101] Add Pedesigner (#41803) --------- Co-authored-by: Vered Kunik --- recipes/pedesigner/meta.yaml | 38 ++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 recipes/pedesigner/meta.yaml diff --git a/recipes/pedesigner/meta.yaml b/recipes/pedesigner/meta.yaml new file mode 100644 index 0000000000000..c29d3896d1bd5 --- /dev/null +++ b/recipes/pedesigner/meta.yaml @@ -0,0 +1,38 @@ +{% set name = "pedesigner" %} +{% set version = "0.2.0" %} +{% set sha256 = "87e95b3985e087c13895243682595bcd8f051f62a5039455be2b9b3ea2c90cbc" %} + +package: + name: {{ name }} + version: {{ version }} + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -vv . + +source: + url: https://github.com/VeredKunik/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +requirements: + build: + - python >=3.7 + + run: + - python >=3.7 + - cas-offinder + +test: + commands: + - pedesigner --help + +about: + home: https://github.com/VeredKunik/pedesigner + license: GPL-3.0-only + license_family: GPL + summary: "A tool for prime-editing guideRNA (pegRNA) design" + +extra: + recipe-maintainers: + - VeredKunik From 1b99c95d44397a15fcd02b09457200cc9f178d38 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 4 Jul 2023 07:09:50 -0600 Subject: [PATCH 009/101] Update nmrglue to 0.9 (#41361) * Update nmrglue to 0.9 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/nmrglue/meta.yaml | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/recipes/nmrglue/meta.yaml b/recipes/nmrglue/meta.yaml index 24ffb2c4fbb6f..95067ffa1f6a0 100644 --- a/recipes/nmrglue/meta.yaml +++ b/recipes/nmrglue/meta.yaml @@ -1,13 +1,18 @@ +{% set name = "nmrglue" %} +{% set version = "0.9" %} +{% set sha256 = "be2602a08b4453bccd2b276640ebe2f06e1598aa3883492be7d11c686f623507" %} + package: - name: nmrglue - version: "0.8" + name: {{ name }} + version: {{ version }} source: - url: https://files.pythonhosted.org/packages/19/f8/75c08a1aca99471c13d20da44cbab2f4c8674de54cff249b3b2e47e5f87a/nmrglue-0.8.tar.gz - sha256: 198375ce724ab9776953a3d3ed3eb4fa0d1b859fac97360cffa5d9143f8a5bfe + url: https://files.pythonhosted.org/packages/5e/64/33f04fc1487b1606a7888c0eb75a53ddd73d83b3ed16a6dc9f6b211e2456/nmrglue-{{ version }}.tar.gz + sha256: {{ sha256 }} build: - number: 5 + number: 0 + skip: True # [py2k] script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: @@ -19,7 +24,7 @@ requirements: run: - python - numpy - - scipy <1.8.0 + - scipy test: imports: @@ -32,6 +37,7 @@ test: about: home: http://www.nmrglue.com - license: BSD License + license: BSD-3-Clause summary: 'A module for working with NMR data in Python' license_family: BSD + license_file: LICENSE.txt From 38f81b268f48ccfa0a347b6312aab12a36eea0f1 Mon Sep 17 00:00:00 2001 From: Maarten-vd-Sande Date: Tue, 4 Jul 2023 16:47:47 +0200 Subject: [PATCH 010/101] Update meta.yaml (#41829) --- recipes/seq2science/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seq2science/meta.yaml b/recipes/seq2science/meta.yaml index 68d8a7af50c65..b25500f0c4677 100644 --- a/recipes/seq2science/meta.yaml +++ b/recipes/seq2science/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: host: @@ -24,7 +24,7 @@ requirements: - conda =23.1.0 - mamba =1.2.0 - genomepy =0.15.0 - - biopython =1.81 + - conda-forge::biopython =1.81 - filelock =3.10.7 - pyyaml =6.0 - pandas_schema =0.3.5 From 13d1108ba05f4c5dce55d14c0de6e6d8f205bb88 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 4 Jul 2023 09:54:55 -0600 Subject: [PATCH 011/101] Update annonars to 0.12.8 (#41826) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 06279afd2d879..18984e86e4d4a 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.12.7" %} +{% set version = "0.12.8" %} package: name: annonars @@ -10,7 +10,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 769a95422791f82132aef9154d98ab15b79797baf90b299ff1a358750fd951fb + sha256: 5a1087440f0b136b2c1a4d5fb884fd2af15744831bf77636e3767ba416ed1df8 requirements: build: From 64baeddd61d0431ddc33713b87d6a49d86de721b Mon Sep 17 00:00:00 2001 From: Julianus Pfeuffer Date: Tue, 4 Jul 2023 22:25:45 +0200 Subject: [PATCH 012/101] [Update] Enable OpenMS for macOS again (#41824) * [Update] Enable OpenMS for macOS again * remove skip completely of course * remove associated comment --- recipes/openms-meta/meta.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/recipes/openms-meta/meta.yaml b/recipes/openms-meta/meta.yaml index f53e76e83489f..60a9477d4f475 100644 --- a/recipes/openms-meta/meta.yaml +++ b/recipes/openms-meta/meta.yaml @@ -7,11 +7,9 @@ package: source: url: https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/{{ version }}/OpenMS-{{ version }}-src.tar.gz sha256: 2d186f35fe42573a19283605ccfb491ca6da585880fa3725a013975df26bc008 - -# osx currently skipped because of https://github.com/bioconda/bioconda-recipes/issues/41526 + build: - number: 3 - skip: True # [osx] + number: 4 # Try this when building with GUI #extra: From 112305e962914c9c25556fd6fa6effdc6d2d7f8b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 4 Jul 2023 14:28:24 -0600 Subject: [PATCH 013/101] Update tspex to 0.6.3 (#41833) --- recipes/tspex/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tspex/meta.yaml b/recipes/tspex/meta.yaml index c4ab0e433594f..30af6c194d481 100644 --- a/recipes/tspex/meta.yaml +++ b/recipes/tspex/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tspex" %} -{% set version = "0.6.2" %} +{% set version = "0.6.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: bb9a2ac4cc05bc7947ca57ed060ad29015f89748cfde8e9615bac26f439cc474 + sha256: 315bfa1f60ea582777c549313cad9e9da0a4d11c5f69a6fc767bd0823dc46316 build: number: 0 From 64f4f17a35b9c3a8a4a94de8ecae37a851583c40 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 5 Jul 2023 06:24:06 -0600 Subject: [PATCH 014/101] Update microhapdb to 0.9 (#41818) * Update microhapdb to 0.9 * Add pyfaidx dependency * Download reference genome for test build * Fix pyfaidx pin --------- Co-authored-by: Daniel Standage --- recipes/microhapdb/meta.yaml | 5 +++-- recipes/microhapdb/run_test.sh | 2 ++ 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/microhapdb/meta.yaml b/recipes/microhapdb/meta.yaml index d88e24f7d078a..ae8d63485b891 100644 --- a/recipes/microhapdb/meta.yaml +++ b/recipes/microhapdb/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8.2" %} -{% set sha256 = "d21b84765513a1229aaf796dfb4b233653ce0c8028d030db54f3396244d228ca" %} +{% set version = "0.9" %} +{% set sha256 = "ea613bdfa5a90792bb8724469966b55e012194ba49263afdafba5805c4f74d83" %} package: name: microhapdb @@ -23,6 +23,7 @@ requirements: run: - python >=3 - pandas >=1.2 + - pyfaidx >=0.7 test: imports: diff --git a/recipes/microhapdb/run_test.sh b/recipes/microhapdb/run_test.sh index 80a8ac9eb2701..16254d847a721 100755 --- a/recipes/microhapdb/run_test.sh +++ b/recipes/microhapdb/run_test.sh @@ -1,3 +1,5 @@ #!/usr/bin/env bash set -eo pipefail +microhapdb --download pytest --cov=microhapdb --pyargs microhapdb +find $PREFIX -type f -name 'hg38*' -exec rm {} \; From 606df7c24b0e994257daeb4b4ef7f2d13e9e5387 Mon Sep 17 00:00:00 2001 From: Marc Sturm Date: Wed, 5 Jul 2023 17:40:49 +0200 Subject: [PATCH 015/101] Update ngs-bits to version 2023_06 (#41811) * Updated ngs-bits to version 2018_10 * Updated ngs-bits to version 2023_06 * updated build number * updated build command * updated build.sh * added lib path to qmake * update * update --- recipes/ngs-bits/build.sh | 2 +- recipes/ngs-bits/meta.yaml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/ngs-bits/build.sh b/recipes/ngs-bits/build.sh index 7a9bb2def6a22..a3c73b67f42a5 100644 --- a/recipes/ngs-bits/build.sh +++ b/recipes/ngs-bits/build.sh @@ -11,7 +11,7 @@ export PATH=$BUILD_PREFIX/bin/:$PATH #build (enable debug info by adding '-Wall -d') mkdir build cd build -qmake CONFIG-=debug CONFIG+=release DEFINES+=QT_NO_DEBUG_OUTPUT QMAKE_CXX=${CXX} QMAKE_RPATHLINKDIR+=${PREFIX}/lib/ ../src/tools.pro +qmake CONFIG-=debug CONFIG+=release DEFINES+=QT_NO_DEBUG_OUTPUT QMAKE_CXX="$CXX" QMAKE_CC="$CC" QMAKE_CFLAGS="$CFLAGS" QMAKE_CXXFLAGS="$CXXFLAGS" QMAKE_LIBDIR+="$PREFIX/lib" QMAKE_RPATHLINKDIR+=${PREFIX}/lib/ ../src/tools.pro make cd .. diff --git a/recipes/ngs-bits/meta.yaml b/recipes/ngs-bits/meta.yaml index b91be72b8729c..cbac5d063c01a 100755 --- a/recipes/ngs-bits/meta.yaml +++ b/recipes/ngs-bits/meta.yaml @@ -1,15 +1,15 @@ -{% set version = "2023_02" %} +{% set version = "2023_06" %} package: name: ngs-bits version: {{ version }} build: - number: 2 + number: 0 source: url: https://github.com/imgag/ngs-bits/releases/download/{{ version }}/ngs-bits-{{ version }}.tgz - sha256: 9aaf0ac7759c1f8fb3fe7f5bf84f70b235e6c25b45a3f7646f02a4b883f8d784 + sha256: 2b2583f43e9e16a98e45e670ab2d8c195f0c233abf7eaaa0c9b126d8c10d07a3 requirements: build: From c0672f71ba86b29bffd99dfc1486dd90e8a86f15 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 5 Jul 2023 12:08:37 -0600 Subject: [PATCH 016/101] Update varfish-server-worker to 0.9.0 (#41846) --- recipes/varfish-server-worker/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varfish-server-worker/meta.yaml b/recipes/varfish-server-worker/meta.yaml index 044fe8f5d3924..f573b0e22e496 100644 --- a/recipes/varfish-server-worker/meta.yaml +++ b/recipes/varfish-server-worker/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.0" %} +{% set version = "0.9.0" %} package: name: varfish-server-worker @@ -10,7 +10,7 @@ build: source: url: https://github.com/bihealth/varfish-server-worker/archive/refs/tags/v{{ version }}.tar.gz - sha256: 32dda98a4400e15a56410e5540daaa035eedfed6cf36a2fbf4516dd176b16095 + sha256: 37793ae094b01031dfd794b888547b30cc8cbf1a7dbe831a885dabde8e7f5774 requirements: build: From be6c3839eab80935b1af444e20af777b6656e687 Mon Sep 17 00:00:00 2001 From: Leonid Kostrykin Date: Wed, 5 Jul 2023 22:13:08 +0200 Subject: [PATCH 017/101] Update superdsm to 0.1.3 (#41840) * updates superdsm to 0.1.3 * retrigger build * retrigger build --- recipes/superdsm/meta.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/superdsm/meta.yaml b/recipes/superdsm/meta.yaml index 06cb204070a99..74b82f0dfcf60 100644 --- a/recipes/superdsm/meta.yaml +++ b/recipes/superdsm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SuperDSM" %} -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} {% set repo_url = "https://github.com/BMCV/SuperDSM" %} {% set docs_url = "https://superdsm.readthedocs.io" %} @@ -9,10 +9,10 @@ package: source: url: "{{ repo_url }}/archive/refs/tags/v{{ version }}.zip" - sha256: e00e13b9bb330fccc38fb46629b651d541a3ff66339c2b5d3d962811cf375c63 + sha256: f55abbd6818a66886ddfe3f7fd9c5dd93c63ed2b6e3179552106e560a000ad5f build: - number: 1 + number: 0 noarch: python script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv " @@ -33,8 +33,7 @@ requirements: - cvxpy >=1.1.13,<2.0 - matplotlib-base >=3.0,<4.0 - mkl >=2020.0 - - posix_ipc >=1.0.4,<2.0 - - ray-default >=0.8.7 + - ray-core >=0.8.7,<1.7 test: commands: From ed820143e87d33a4674362d0efc00de2fd6b59af Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 5 Jul 2023 15:42:08 -0600 Subject: [PATCH 018/101] Update pybiolib to 1.1.1073 (#41848) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 329abb595ef22..99e5dba470d3d 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1065" %} +{% set version = "1.1.1073" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 62c926afcd0a0ad7b48fd9d9a64d9449779458375a9cdebb20c26a46dfcbee8d + sha256: 880a7289c23746b4b5185c07e144bf75985f1e5b1ffbb17b8e99d14ced183a27 build: noarch: python From 95bbdcfe016ea239abc7e656c20ea58edb84c273 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 5 Jul 2023 18:01:19 -0600 Subject: [PATCH 019/101] Update gtdbtk to 2.3.2 (#41852) * Update gtdbtk to 2.3.2 * Update pydantic version. --------- Co-authored-by: Aaron Mussig --- recipes/gtdbtk/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/gtdbtk/meta.yaml b/recipes/gtdbtk/meta.yaml index 5372d2de260d5..611e22a30947f 100644 --- a/recipes/gtdbtk/meta.yaml +++ b/recipes/gtdbtk/meta.yaml @@ -1,13 +1,13 @@ {% set name = "gtdbtk" %} -{% set version = "2.3.0" %} +{% set version = "2.3.2" %} package: name: {{ name|lower }} version: {{ version }} source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 4f237a03657be4540ac653c276fe31c002b6923af0411316719a9541d6e97d4b + sha256: 80efd31e10007d835f56a3d6fdf039a59db3b6ba4be26b234692da5e688aa99f build: - number: 2 + number: 0 noarch: python entry_points: - gtdbtk = gtdbtk.__main__:main @@ -26,7 +26,7 @@ requirements: - numpy >=1.9.0 - mash >=2.0 - tqdm >=4.35.0 - - pydantic + - pydantic >=1.9.2, <2 test: imports: - gtdbtk From df21a70589a96d5fcaf9cbd0afe3b53073f894cf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 00:42:05 -0600 Subject: [PATCH 020/101] Update shigatyper to 2.0.5 (#41853) --- recipes/shigatyper/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/shigatyper/meta.yaml b/recipes/shigatyper/meta.yaml index 6572b27a51dff..66642b6e2b878 100644 --- a/recipes/shigatyper/meta.yaml +++ b/recipes/shigatyper/meta.yaml @@ -1,10 +1,10 @@ package: name: shigatyper - version: 2.0.4 + version: 2.0.5 source: - url: https://github.com/CFSAN-Biostatistics/shigatyper/archive/refs/tags/conda-package-2.0.4.tar.gz - sha256: 129a0ec7ec83bb9de6d79cf157b401fc16450a7964130c6608e1b618aa13c09d + url: https://github.com/CFSAN-Biostatistics/shigatyper/archive/refs/tags/conda-package-2.0.5.tar.gz + sha256: e853263d70bc557c7a131fac982dcd402afe3aa3fb0fc4c5fde8805b708682f1 build: noarch: python From 26d0212922e2660b249bd89e895d4250e331ca26 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 03:50:22 -0600 Subject: [PATCH 021/101] Update matchms to 0.21.1 (#41784) * Update matchms to 0.21.0 * Update matchms to 0.21.1 --- recipes/matchms/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 242f6a0423352..99e85e308c61f 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "matchms" %} -{% set version = "0.20.0" %} +{% set version = "0.21.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: bb618eef74a23fd336b8e950ade5ecb65f1096d8ddfeced0e01934d20048557f + sha256: 9ef706361b885f8c23e14b470adb3a18fc0b156a0a243b70de8ec998a41e05ba build: number: 0 From 02d4849c0746ef344d17608224991fd8bd55d82d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 04:46:42 -0600 Subject: [PATCH 022/101] Update bioconda-utils to 2.3.3 (#41747) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update bioconda-utils to 2.3.2 * Update bioconda-utils to 2.3.3 * debug * Update meta.yaml --------- Co-authored-by: Björn Grüning Co-authored-by: Devon Ryan --- recipes/bioconda-utils/meta.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index d3f5dc49efa03..88b92564b953e 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.3.1" %} -{% set sha256 = "71cfdf4cfeecb2c1f2ef6b6f45c54407b6e7f0f2a8ae45fc40e51e12b36905a3" %} +{% set version = "2.3.3" %} +{% set sha256 = "aaee4e69f47d732c0e0515358a5a2b4223832a74070e751281af06c19b4dda3f" %} package: name: bioconda-utils @@ -23,7 +23,7 @@ requirements: run: - python >=3.7 - conda 23.3.* - - boa 0.14.* + - boa 0.15.* - conda-build 3.24.* - conda-verify 3.1.* - argh 0.26.* @@ -85,8 +85,7 @@ test: "${PREFIX}/bin/conda" install --prefix="${PREFIX}" --dry-run --satisfied-skip-solve --file="$( python -c 'from os.path import dirname, join; import bioconda_utils; print(join(dirname(bioconda_utils.__file__), "bioconda_utils-requirements.txt"))' - )" - 2>&1 | grep -qF 'All requested packages already installed.' + )" 2>&1 | grep -qF 'All requested packages already installed.' about: home: http://bioconda.github.io/build-system.html From bd9e3c46f797f06f3834e60401faa0e76349c83f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 05:18:45 -0600 Subject: [PATCH 023/101] Update kallisto to 0.50.0 (#41699) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update kallisto to 0.50.0 * Update meta * Attempt to update build recipe * Include bzip2 and xz for compression handling --------- Co-authored-by: Michael Steinbaugh Co-authored-by: Johannes Köster --- recipes/kallisto/build.sh | 17 ++- recipes/kallisto/build_failure.linux-64.yaml | 104 ------------------- recipes/kallisto/build_failure.osx-64.yaml | 104 ------------------- recipes/kallisto/meta.yaml | 12 ++- 4 files changed, 16 insertions(+), 221 deletions(-) delete mode 100644 recipes/kallisto/build_failure.linux-64.yaml delete mode 100644 recipes/kallisto/build_failure.osx-64.yaml diff --git a/recipes/kallisto/build.sh b/recipes/kallisto/build.sh index 6c2dd25276e96..b797c382d4071 100644 --- a/recipes/kallisto/build.sh +++ b/recipes/kallisto/build.sh @@ -1,15 +1,12 @@ #!/bin/bash -cd ext/htslib -autoreconf -cd ../.. - - -mkdir -p $PREFIX/bin - +cd ext/htslib || exit 1 +autoreconf --force --install --verbose +./configure +cd ../.. || exit 1 +mkdir -p "${PREFIX}/bin" mkdir -p build -cd build - -cmake -DCMAKE_INSTALL_PREFIX:PATH=$PREFIX .. -DUSE_HDF5=ON +cd build || exit 1 +cmake -DCMAKE_INSTALL_PREFIX:PATH="$PREFIX" .. -DUSE_HDF5=ON make make install diff --git a/recipes/kallisto/build_failure.linux-64.yaml b/recipes/kallisto/build_failure.linux-64.yaml deleted file mode 100644 index 65243c6acdbd7..0000000000000 --- a/recipes/kallisto/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: d2ce538a5f252b13e2bdb61ff0352bde2a0d74612792647dbafcf02a4120f347 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit - GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof - LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld - LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold - NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm - OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy - OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump - RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib - READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf - SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size - STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings - STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip - INFO: activate-gcc_linux-64.sh made the following environmental changes: - BUILD=x86_64-conda-linux-gnu - CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr - CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot - CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu - CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu - CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp - CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include - DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include - GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc - GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar - GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm - GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib - HOST=x86_64-conda-linux-gnu - LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu - build_alias=x86_64-conda-linux-gnu - host_alias=x86_64-conda-linux-gnu - -BUILD=x86_64-conda_cos6-linux-gnu - -CONDA_BUILD_SYSROOT= - INFO: activate-gxx_linux-64.sh made the following environmental changes: - CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g - perl: warning: Setting locale failed. - perl: warning: Please check that your locale settings: - LANGUAGE = (unset), - LC_ALL = (unset), - LANG = "C.UTF-8" - are supported and installed on your system. - perl: warning: Falling back to the standard locale ("C"). - perl: warning: Setting locale failed. - perl: warning: Please check that your locale settings: - LANGUAGE = (unset), - LC_ALL = (unset), - LANG = "C.UTF-8" - are supported and installed on your system. - perl: warning: Falling back to the standard locale ("C"). - perl: warning: Setting locale failed. - perl: warning: Please check that your locale settings: - LANGUAGE = (unset), - LC_ALL = (unset), - LANG = "C.UTF-8" - are supported and installed on your system. - perl: warning: Falling back to the standard locale ("C"). - perl: warning: Setting locale failed. - perl: warning: Please check that your locale settings: - LANGUAGE = (unset), - LC_ALL = (unset), - LANG = "C.UTF-8" - are supported and installed on your system. - perl: warning: Falling back to the standard locale ("C"). - perl: warning: Setting locale failed. - perl: warning: Please check that your locale settings: - LANGUAGE = (unset), - LC_ALL = (unset), - LANG = "C.UTF-8" - are supported and installed on your system. - perl: warning: Falling back to the standard locale ("C"). - configure.ac: error: required file 'config.sub' not found - configure.ac: error: required file 'config.guess' not found - configure.ac: try running autoreconf --install - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/kallisto_1685523137285/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/kallisto/build_failure.osx-64.yaml b/recipes/kallisto/build_failure.osx-64.yaml deleted file mode 100644 index d9ec798831a08..0000000000000 --- a/recipes/kallisto/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: d2ce538a5f252b13e2bdb61ff0352bde2a0d74612792647dbafcf02a4120f347 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - libxml2: 2.11.4-hd95e348_0 conda-forge - libzlib: 1.2.13-hfd90126_4 conda-forge - llvm-tools: 15.0.7-he4b1e75_2 conda-forge - m4: 1.4.18-haf1e3a3_1001 conda-forge - make: 4.3-h22f3db7_1 conda-forge - ncurses: 6.3-h96cf925_1 conda-forge - openssl: 3.1.1-h8a1eda9_1 conda-forge - perl: 5.32.1-2_h0d85af4_perl5 conda-forge - rhash: 1.4.3-hac89ed1_0 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - zlib: 1.2.13-hfd90126_4 conda-forge - zstd: 1.5.2-hbc0c0cd_6 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - Downloading source to cache: v0.48.0_1797ac4d1f.tar.gz - Downloading https://github.com/pachterlab/kallisto/archive/v0.48.0.tar.gz - INFO:conda_build.source:Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - INFO:conda_build.source:Downloading source to cache: v0.48.0_1797ac4d1f.tar.gz - INFO:conda_build.source:Downloading https://github.com/pachterlab/kallisto/archive/v0.48.0.tar.gz - Success - INFO:conda_build.source:Success - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/kallisto_1685525877786/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/kallisto_1685525877786/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/kallisto_1685525877786/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/kallisto_1685525877786/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - configure.ac: error: required file 'config.sub' not found - configure.ac: error: required file 'config.guess' not found - configure.ac: try running autoreconf --install - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/kallisto_1685525877786/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/kallisto/meta.yaml b/recipes/kallisto/meta.yaml index 7c058895f8de8..c312886ba195e 100644 --- a/recipes/kallisto/meta.yaml +++ b/recipes/kallisto/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.48.0" %} +{% set version = "0.50.0" %} package: name: kallisto @@ -6,10 +6,10 @@ package: source: url: https://github.com/pachterlab/kallisto/archive/v{{ version }}.tar.gz - sha256: 1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0 + sha256: f9cc0058d08206cb6dde4a4dcaf8a778df5a939a6e021508eea9b00b0d6d5368 build: - number: 3 + number: 0 requirements: build: @@ -19,10 +19,14 @@ requirements: - autoconf - automake host: + - bzip2 - hdf5 + - xz - zlib run: + - bzip2 - hdf5 + - xz - zlib test: @@ -38,5 +42,7 @@ extra: identifiers: - biotools:kallisto - doi:10.1038/nbt.3519 + recipe-maintainers: + - mjsteinbaugh skip-lints: - missing_tests From 125588790c1cdb3c6103beb58008241a858d527b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 06:04:16 -0600 Subject: [PATCH 024/101] Update expam to 1.2.2 (#41350) * Update expam to 1.2.2 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/expam/meta.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/recipes/expam/meta.yaml b/recipes/expam/meta.yaml index 114aac9de645e..573f9fe24a580 100644 --- a/recipes/expam/meta.yaml +++ b/recipes/expam/meta.yaml @@ -1,5 +1,5 @@ {% set name = "expam" %} -{% set version = "1.2.0" %} +{% set version = "1.2.2" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 40cda1a82ff1238fe77668b5527fb8a9ba082f7738dcb06b06970859f4aceea4 + sha256: 8c527a4d320364173cd067333c5923893d9c93d942945374f62cd6f0c6b809c6 build: - number: 2 + number: 0 skip: true # [py < 38] script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " @@ -21,12 +21,13 @@ requirements: - pip - python - cython - - numpy>=1.22.0 + - numpy >=1.22.0 - setuptools >=46.4 run: - python - - numpy>=1.22.0 + - numpy >=1.22.0 - matplotlib-base + - multiprocess - pandas - psutil - requests From e4dc77693de7dea5d0ffb6d09044af36983917d3 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 06:31:53 -0600 Subject: [PATCH 025/101] Update svhip to 1.0.9 (#41858) * Update svhip to 1.0.9 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/svhip/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/svhip/meta.yaml b/recipes/svhip/meta.yaml index c389036662cd1..b74c840d4656c 100644 --- a/recipes/svhip/meta.yaml +++ b/recipes/svhip/meta.yaml @@ -1,6 +1,5 @@ -{% set version = "1.0.8" %} -{% set sha256 = "86d4fce71f8af2952b30bc300f760167425ff24aaf3ebe053a07bb543bed04a4" %} - +{% set version = "1.0.9" %} +{% set sha256 = "166da6643437a63b842a85b570d2d7a061cd5d7916e7baef89eddc284d0ad8d8" %} package: name: "svhip" @@ -32,5 +31,6 @@ test: about: home: https://github.com/chrisBioInf/Svhip license: MIT + license_family: MIT license_file: LICENSE summary: Retrainable machine learning pipeline for the detection of secondary structure conservation on a genome-level. From 8f09ea033db25d2721ce4f50dbcde11375fb9ccd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Guizard?= Date: Thu, 6 Jul 2023 15:09:29 +0100 Subject: [PATCH 026/101] Replace Strobemap and slamem by namfinder (#41862) --- recipes/ultra_bioinformatics/meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/recipes/ultra_bioinformatics/meta.yaml b/recipes/ultra_bioinformatics/meta.yaml index a3867135d64dd..a89656b216def 100644 --- a/recipes/ultra_bioinformatics/meta.yaml +++ b/recipes/ultra_bioinformatics/meta.yaml @@ -10,7 +10,7 @@ source: sha256: c477b526cba52fcaf369efb67f0d0096ea1702d7adc8457746a91ae5f750a0ef build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . -vv" @@ -32,10 +32,9 @@ requirements: - parasail-python - pysam - python - - slamem - mummer - minimap2 - - strobemap + - namfinder test: imports: From 148612d4e81502a0efd5bba2c7688e76540d3228 Mon Sep 17 00:00:00 2001 From: Jessica Mattick <19544292+jmattick@users.noreply.github.com> Date: Thu, 6 Jul 2023 13:44:12 -0700 Subject: [PATCH 027/101] Update pbpigeon to v1.1.0 (#41850) * Update pbpigeon to v1.1.0 * Update build number --------- Co-authored-by: Jessica Mattick --- recipes/pbpigeon/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pbpigeon/meta.yaml b/recipes/pbpigeon/meta.yaml index 88c3e0d525dfc..ee74d485d69a8 100644 --- a/recipes/pbpigeon/meta.yaml +++ b/recipes/pbpigeon/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pbpigeon" %} -{% set version = "1.0.0" %} +{% set version = "1.1.0" %} package: name: {{ name }} @@ -7,12 +7,12 @@ package: source: - url: https://github.com/PacificBiosciences/pigeon/releases/download/v{{ version }}/pigeon - sha256: 1b1dca433acea6bc7a6f919da2ab4e404112e9dd503e5b209251ed3296af2d50 + sha256: d35b090536ef2d9e9af5a6a5e91ccd87bc5214a275d88a145c73fdc74374c0f4 build: # repackaged binaries skip: True # [osx] - number: 2 + number: 0 requirements: build: From c30685892ca02a9b890da794292f8b53231c50a1 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 6 Jul 2023 16:17:39 -0500 Subject: [PATCH 028/101] Update nrpys recipe to build shared python module (#41538) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update nrpys recipe to build shared python module * fix typos * Update recipes/nrpys/meta.yaml Co-authored-by: Björn Grüning * try noarch:generic --------- Co-authored-by: Björn Grüning --- recipes/nrpys/build.sh | 11 ++++------- recipes/nrpys/meta.yaml | 25 ++++++++++++------------- recipes/nrpys/patch | 15 +++++++++++++++ 3 files changed, 31 insertions(+), 20 deletions(-) create mode 100644 recipes/nrpys/patch diff --git a/recipes/nrpys/build.sh b/recipes/nrpys/build.sh index 241d7bb635685..c08897288c011 100644 --- a/recipes/nrpys/build.sh +++ b/recipes/nrpys/build.sh @@ -4,14 +4,11 @@ # We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" -export HOME=${PREFIX} - -export C_INCLUDE_PATH=${PREFIX}/include +export INCLUDE_PATH=${PREFIX}/include export LIBRARY_PATH=${PREFIX}/lib mkdir -p ${PREFIX}/bin -# build statically linked binary with Rust -maturin build --release -f -pip install -vv -e . -cp ${SRC_DIR}/python/nrpys/nrpys.*.so ${PREFIX}/lib/libnrpys.so +# build shared Python module with Rust +maturin build --release --strip -f +${PYTHON} -m pip install -vv . diff --git a/recipes/nrpys/meta.yaml b/recipes/nrpys/meta.yaml index d2e1bfcb676c3..587bb75ae1e65 100644 --- a/recipes/nrpys/meta.yaml +++ b/recipes/nrpys/meta.yaml @@ -7,32 +7,31 @@ package: version: {{ version }} build: - skip: True # [py < 38] - number: 0 + number: 1 + noarch: generic source: url: https://github.com/kblin/nrpys/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} + patch: + - patch requirements: - build: - - rust - - {{ compiler('c') }} host: - - zlib - - python + - python >=3.7 - pip + - rust - maturin + - zlib run: - - python + - python >=3.7 test: - commands: - - "ls ${PREFIX}/lib/libnrpys.so" + imports: + - nrpys about: - home: https://github.com/kblin/nrpys + home: "https://github.com/kblin/nrpys" license: GPL3 license_file: LICENSE.txt - summary: | - Python language bindings for nrps-rs substrate specificity predictor. + summary: "Python language bindings for nrps-rs substrate specificity predictor." diff --git a/recipes/nrpys/patch b/recipes/nrpys/patch new file mode 100644 index 0000000000000..99ab333ca033e --- /dev/null +++ b/recipes/nrpys/patch @@ -0,0 +1,15 @@ +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -1,5 +1,5 @@ + [build-system] +-requires = ["maturin>=0.14,<0.15"] ++requires = ["maturin>=1.0,<2.0"] + build-backend = "maturin" + + [project] +@@ -13,3 +13,5 @@ classifiers = [ + + [tool.maturin] + python-source = "python" ++features = ["pyo3/extension-module"] ++cargo-extra-args = "--features extension-module" From 79afd8efc40d1b89bff74327539222054c150139 Mon Sep 17 00:00:00 2001 From: Timo Sachsenberg Date: Thu, 6 Jul 2023 23:47:49 +0200 Subject: [PATCH 029/101] Update pyopenms recipe to fix zlib issue (#41716) * Update meta.yaml * update build number * Update meta.yaml * Update recipes/pyopenms/meta.yaml Co-authored-by: Julianus Pfeuffer --------- Co-authored-by: Julianus Pfeuffer --- recipes/pyopenms/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/pyopenms/meta.yaml b/recipes/pyopenms/meta.yaml index d65dfc36ff1dd..f01379c5d99c1 100644 --- a/recipes/pyopenms/meta.yaml +++ b/recipes/pyopenms/meta.yaml @@ -10,20 +10,21 @@ source: build: skip: True # [py2k] - number: 2 + number: 3 requirements: build: - {{ compiler('cxx') }} - make - cmake + - sysroot_linux-64 =2.17 # [linux] host: - libopenms {{ version }} - llvm-openmp # [osx] - libsvm - xerces-c - boost-cpp - - qt + - qt-main - python {{ python }} - cython >=0.25.2 - autowrap >=0.22.10 @@ -33,17 +34,19 @@ requirements: - numpy {{ numpy }} - pandas - matplotlib-base + - sysroot_linux-64 =2.17 # [linux] run: # run_exports in libopenms should take care of the libraries. But it does not because of bugs. So copy everthing again and again - libopenms {{ version }} - llvm-openmp # [osx] - libsvm - xerces-c - boost-cpp - - qt + - qt-main - python {{ python }} - numpy {{ numpy }} - pandas - matplotlib-base + - sysroot_linux-64 =2.17 # [linux] test: commands: - python -c "import pyopenms; print(pyopenms.__version__)" From 8bcf8d977b035818f6bc2314c3f07c38d20793a6 Mon Sep 17 00:00:00 2001 From: Michael Steinbaugh Date: Thu, 6 Jul 2023 21:25:24 -0400 Subject: [PATCH 030/101] Add r-wormbase 0.4.1 (#41863) --- recipes/r-wormbase/build.sh | 1 + recipes/r-wormbase/meta.yaml | 68 ++++++++++++++++++++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 recipes/r-wormbase/build.sh create mode 100644 recipes/r-wormbase/meta.yaml diff --git a/recipes/r-wormbase/build.sh b/recipes/r-wormbase/build.sh new file mode 100644 index 0000000000000..5bf492ab9fc06 --- /dev/null +++ b/recipes/r-wormbase/build.sh @@ -0,0 +1 @@ +$R CMD INSTALL --build . diff --git a/recipes/r-wormbase/meta.yaml b/recipes/r-wormbase/meta.yaml new file mode 100644 index 0000000000000..a1da5c9edf406 --- /dev/null +++ b/recipes/r-wormbase/meta.yaml @@ -0,0 +1,68 @@ +{% set version = "0.4.1" %} +{% set github = "https://github.com/acidgenomics/r-wormbase" %} + +package: + name: r-wormbase + version: "{{ version }}" + +source: + url: "{{ github }}/archive/v{{ version }}.tar.gz" + sha256: 73d222e37d90331a8d37e3aeae9efc9b88646cdeb7d394a698334eed8a13ae2a + +build: + number: 0 + noarch: generic + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + # Depends: + - r-base + # Imports: + - bioconductor-biocgenerics >=0.44.0 + - bioconductor-iranges >=2.32.0 + - bioconductor-s4vectors >=0.36.0 + - r-acidbase >=0.6.16 + - r-acidcli >=0.2.7 + - r-acidgenerics >=0.6.7 + - r-acidplyr >=0.3.10 + - r-goalie >=0.6.10 + - r-httr2 >=0.2.3 + - r-pipette >=0.10.10 + - r-stringi >=1.7.12 + - r-syntactic >=0.6.6 + run: + # Depends: + - r-base + # Imports: + - bioconductor-biocgenerics >=0.44.0 + - bioconductor-iranges >=2.32.0 + - bioconductor-s4vectors >=0.36.0 + - r-acidbase >=0.6.16 + - r-acidcli >=0.2.7 + - r-acidgenerics >=0.6.7 + - r-acidplyr >=0.3.10 + - r-goalie >=0.6.10 + - r-httr2 >=0.2.3 + - r-pipette >=0.10.10 + - r-stringi >=1.7.12 + - r-syntactic >=0.6.6 + +test: + commands: + - $R -e "library('WormBase')" + +about: + home: https://r.acidgenomics.com/packages/wormbase/ + dev_url: "{{ github }}" + license: AGPL-3.0 + license_file: LICENSE + license_family: GPL + summary: Fetch Caenorhabditis elegans genome annotations from WormBase. + +extra: + recipe-maintainers: + - acidgenomics + - mjsteinbaugh From a0a41aa504dd69e8f786b2c9ddc2c289da2c5de4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jo=C3=A3o=20Vitor?= Date: Thu, 6 Jul 2023 22:25:43 -0300 Subject: [PATCH 031/101] Add Verticall recipe (#41860) --- recipes/verticall/meta.yaml | 51 +++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 recipes/verticall/meta.yaml diff --git a/recipes/verticall/meta.yaml b/recipes/verticall/meta.yaml new file mode 100644 index 0000000000000..81e5cae2549c5 --- /dev/null +++ b/recipes/verticall/meta.yaml @@ -0,0 +1,51 @@ +{% set name = "Verticall" %} +{% set version = "0.4.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/rrwick/Verticall/archive/v{{ version }}.tar.gz + sha256: 13d1a2013611b1061530e473dcd2c4f888cb38d2f2e3e9b85a4837a36f4278d7 + +build: + entry_points: + - verticall = verticall.__main__:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv + number: 0 + +requirements: + host: + - python >=3.7 + - pip + run: + - python >=3.7 + - numpy + - pandas + - matplotlib-base + - plotnine + - pytest + - svgwrite + - minimap2 + +test: + imports: + - verticall + commands: + - pip check + - verticall --help + - minimap2 --help + requires: + - pip + +about: + home: https://github.com/rrwick/Verticall + license: GPL-3.0 + license_file: LICENSE + summary: "A tool for building recombination-free trees" + +extra: + recipe-maintainers: + - jvfe From 1c2ff7a9dc17e9068a2501937198732c89a35616 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 19:25:56 -0600 Subject: [PATCH 032/101] Update deeplc to 2.2.4 (#41856) --- recipes/deeplc/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/deeplc/meta.yaml b/recipes/deeplc/meta.yaml index 4f74e8720c649..bbcc305e23a1c 100644 --- a/recipes/deeplc/meta.yaml +++ b/recipes/deeplc/meta.yaml @@ -1,6 +1,6 @@ {% set name = "DeepLC" %} -{% set version = "2.2.3" %} -{% set sha256 = "264e832684e4d902dc244b3be1aa680f25c7c4a8e76bb28fae730835e6411367" %} +{% set version = "2.2.4" %} +{% set sha256 = "d5795e3b69ecfafbbf796026638c50d3481ffb0be058a0c46c9c11f957c50993" %} package: name: {{ name|lower }} From 82369719344a2310a20e5871bec2b67d078bc2d9 Mon Sep 17 00:00:00 2001 From: Brandon Seah Date: Fri, 7 Jul 2023 03:27:13 +0200 Subject: [PATCH 033/101] Add gnparser 1.7.3 (#41867) * Add gnparser 1.7.3 * Add home url --- recipes/gnparser/build.sh | 8 ++++++++ recipes/gnparser/meta.yaml | 35 +++++++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 recipes/gnparser/build.sh create mode 100644 recipes/gnparser/meta.yaml diff --git a/recipes/gnparser/build.sh b/recipes/gnparser/build.sh new file mode 100644 index 0000000000000..cac558fdb6ebb --- /dev/null +++ b/recipes/gnparser/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +cd gnparser +CGO_ENABLED=0 +go clean +go build . +mkdir -p $PREFIX/bin +mv gnparser $PREFIX/bin diff --git a/recipes/gnparser/meta.yaml b/recipes/gnparser/meta.yaml new file mode 100644 index 0000000000000..91f8b8890b40f --- /dev/null +++ b/recipes/gnparser/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.7.3" %} +{% set sha256 = "40813d180b8ab078b52fcd0ba4be6e0aae5f462afabbb6b5d360638d833cd4eb" %} + +package: + name: "gnparser" + version: {{ version }} + +source: + url: + - https://github.com/gnames/gnparser/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - {{ compiler('go') }} + +test: + commands: + - gnparser -V + - gnparser "Homo sapiens Linnaeus 1758" + +about: + home: https://parser.globalnames.org/ + dev_url: https://github.com/gnames/gnparser + license: MIT + license_file: LICENSE + summary: "GNparser normalises scientific names and extracts their semantic elements" + + +extra: + identifiers: + - doi:https://doi.org/10.5281/zenodo.5111569 From f2273f873588825e30b71e0aed3aad379755c10a Mon Sep 17 00:00:00 2001 From: Parham Kazemi Date: Thu, 6 Jul 2023 18:27:25 -0700 Subject: [PATCH 034/101] Update meta.yaml (#41866) --- recipes/btllib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/btllib/meta.yaml b/recipes/btllib/meta.yaml index a3b06b045a198..7e5179de80cf8 100644 --- a/recipes/btllib/meta.yaml +++ b/recipes/btllib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "btllib" %} -{% set version = "1.6.1" %} +{% set version = "1.6.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/bcgsc/btllib/releases/download/v{{ version }}/{{ name|lower }}-{{ version }}.tar.gz - sha256: e391f56ce03f95789f7214d8d4a276892c5303b53f5a3ebf8479cc8547cc3384 + sha256: 06af0bccd68443bc6351d1d6d46599ae2a6e94752ae5fdf973067a77740d751c build: skip: true # [py < 38 or win] From 343ecdbb67d2e8aafefe71cd0fe307fde77ac9b0 Mon Sep 17 00:00:00 2001 From: Eric Roberts Date: Thu, 6 Jul 2023 21:28:17 -0400 Subject: [PATCH 035/101] Remove extra libs from being linked in with gmtk build (#41868) --- recipes/gmtk/build.sh | 1 - recipes/gmtk/meta.yaml | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/gmtk/build.sh b/recipes/gmtk/build.sh index 366ad52bce356..81c308ac329e3 100644 --- a/recipes/gmtk/build.sh +++ b/recipes/gmtk/build.sh @@ -1,5 +1,4 @@ #!/bin/sh -export LD_LIBRARY_PATH=${PREFIX}/lib BASE_CC=$(basename $CXX) DIR_CC=$(dirname $CXX) diff --git a/recipes/gmtk/meta.yaml b/recipes/gmtk/meta.yaml index e1ab663c254e5..030654ccfc30d 100644 --- a/recipes/gmtk/meta.yaml +++ b/recipes/gmtk/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.4.4" build: - number: 13 + number: 14 skip: True # [osx] source: From 8969ee6c1811ea3a23744c69c94156a72a11824e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 19:31:19 -0600 Subject: [PATCH 036/101] Update bellmans-gapc to 2023.07.05 (#41851) --- recipes/bellmans-gapc/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bellmans-gapc/meta.yaml b/recipes/bellmans-gapc/meta.yaml index 48de06df35454..f929e5c91ba7e 100644 --- a/recipes/bellmans-gapc/meta.yaml +++ b/recipes/bellmans-gapc/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2022.07.04" %} +{% set version = "2023.07.05" %} package: name: bellmans-gapc @@ -6,10 +6,10 @@ package: source: url: https://github.com/jlab/gapc/archive/{{ version }}.tar.gz - sha256: 278a942fd760f5c660f50798f8a46e0a8d692fe99b5cfd7f33212daec298d077 + sha256: 05ebe0707c767dc80f0f9a67d5387a098bcf6bf2e26408c5f2059f373410df69 build: - number: 2 + number: 0 requirements: build: From d162396e3b80282a9ade8e621d8f640d639f2e8c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 19:32:15 -0600 Subject: [PATCH 037/101] Update evofr to 0.1.20 (#41871) --- recipes/evofr/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/evofr/meta.yaml b/recipes/evofr/meta.yaml index 9a97b22a8f680..c072a58143a4f 100644 --- a/recipes/evofr/meta.yaml +++ b/recipes/evofr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.19" %} +{% set version = "0.1.20" %} package: name: evofr @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/e/evofr/evofr-{{ version }}.tar.gz - sha256: cdaeaf0090159a5b551345d0e5a819b3551d2c20497c8aad542659f646379306 + sha256: eda7eb5f841ed773b0f4b7f12749bc95231ffc54854016932282db7770329ddc build: number: 0 From 4a5a1456437301343551574c202bd6a20e482ff5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 19:32:31 -0600 Subject: [PATCH 038/101] Update open-cravat to 2.4.0 (#41869) --- recipes/open-cravat/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/open-cravat/meta.yaml b/recipes/open-cravat/meta.yaml index cddcac7b1e157..36009b7f7d949 100644 --- a/recipes/open-cravat/meta.yaml +++ b/recipes/open-cravat/meta.yaml @@ -1,5 +1,5 @@ {% set name = "open-cravat" %} -{% set version = "2.3.1" %} +{% set version = "2.4.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 9a93671a72def00e54f0620b154830cba5f0360f972383c2b78fa8cf8422f850 + sha256: 8fc33e3dd636fd461099542e32ad7723317e6be6a38936c1d87803cb2573ae41 build: number: 0 From 2a14d090333617f753ea138920fbbf2ed18beb57 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 6 Jul 2023 20:33:38 -0500 Subject: [PATCH 039/101] Update searchgui to 4.2.17 (#41838) --- recipes/searchgui/build.sh | 3 --- recipes/searchgui/meta.yaml | 6 +++--- recipes/searchgui/searchgui.py | 2 +- 3 files changed, 4 insertions(+), 7 deletions(-) diff --git a/recipes/searchgui/build.sh b/recipes/searchgui/build.sh index c78ef2b4295ec..c16005eb8e9e8 100644 --- a/recipes/searchgui/build.sh +++ b/recipes/searchgui/build.sh @@ -23,8 +23,5 @@ ln -sf "$(which metamorpheus)" "$outdir"'/resources/MetaMorpheus/metamorpheus' rm -f "$outdir"'/resources/makeblastdb/linux/linux_64bit/makeblastdb' ln -sf "$(which makeblastdb)" "$outdir"'/resources/makeblastdb/linux/linux_64bit/makeblastdb' -# removing MsAmanda prebuilt binary for macosx until .NET Core 6 is released -# rm -f "$outdir"'/resources/MS Amanda/osx/'* - # allowing to write temporary files in resources folder chmod -R a+rw "$outdir"'/resources/' diff --git a/recipes/searchgui/meta.yaml b/recipes/searchgui/meta.yaml index 67a3fd364b099..820357c2977d5 100644 --- a/recipes/searchgui/meta.yaml +++ b/recipes/searchgui/meta.yaml @@ -1,7 +1,7 @@ # Do not forget to update the version string in the searchgui.py file {% set name = "SearchGUI" %} -{% set version = "4.2.14" %} -{% set sha256 = "75b9480ed8dde4945e3c09a89f40440b5e3ceeb97a9f972e26f7d6ee7cb0618e" %} +{% set version = "4.2.17" %} +{% set sha256 = "cd47cd211626ff864d1508062f12c2a38557251bb0f30a32ccdafe30c385fe85" %} {% set build = "0" %} package: @@ -22,7 +22,7 @@ requirements: host: - xtandem ==15.12.15.2 - metamorpheus ==1.0.2 - - blast ==2.12.0 + - blast >=2.14.0 run: - python - openjdk >=17 diff --git a/recipes/searchgui/searchgui.py b/recipes/searchgui/searchgui.py index 99f9086045318..7f0398868d092 100755 --- a/recipes/searchgui/searchgui.py +++ b/recipes/searchgui/searchgui.py @@ -14,7 +14,7 @@ from os import getenv from os import X_OK -jar_file = 'SearchGUI-4.2.14.jar' +jar_file = 'SearchGUI-4.2.17.jar' default_jvm_mem_opts = ['-Xms2g', '-Xmx4g'] From 4c9083c52d31a50a1ac47b62cedcb729f42fa987 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 19:34:10 -0600 Subject: [PATCH 040/101] Update mehari to 0.6.0 (#41834) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index ffdc65aeefb57..5ee9d6f0add62 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.5.7" %} -{% set sha256 = "16f0eefaa9578476a6e40e456095d7f096dda652c1d63be2c6ed0aa65a6587f0" %} +{% set version = "0.6.0" %} +{% set sha256 = "4d64a4e20cb0600550625968f732e1ee09d23be02af2469d46d3160e00966ce2" %} package: name: mehari From 3508a3609173da00ccad1ae52e8cbb3aef0f8034 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 19:34:18 -0600 Subject: [PATCH 041/101] Update perl-module-scandeps to 1.32 (#41847) --- recipes/perl-module-scandeps/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-module-scandeps/meta.yaml b/recipes/perl-module-scandeps/meta.yaml index 7177d54719c66..98f2e51bb16d0 100644 --- a/recipes/perl-module-scandeps/meta.yaml +++ b/recipes/perl-module-scandeps/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-module-scandeps" %} -{% set version = "1.31" %} -{% set sha256 = "fc4d98d2b0015745f3b55b51ddf4445a73b069ad0cb7ec36d8ea781d61074d9d" %} +{% set version = "1.32" %} +{% set sha256 = "7ab3556ccaa812298da33f0a0515037cd513b9e72c42a76d2c2e4d28832215f0" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/R/RS/RSCHUPP/Module-ScanDeps-1.31.tar.gz + url: https://cpan.metacpan.org/authors/id/R/RS/RSCHUPP/Module-ScanDeps-1.32.tar.gz sha256: {{ sha256 }} build: From 6d1de9ce8e899056a7f5950a5364d842b247566c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Crist=C3=B3bal=20Gallardo?= Date: Fri, 7 Jul 2023 03:53:58 +0200 Subject: [PATCH 042/101] Add myTAI R package (#41628) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Add recipe * Update recipe * Update recipe * Update recipe * Add armadillo * Add r-textshaping library * add harfbuzz and fribidi as host dependency * Update_recipe * Update recipes/r-mytai/meta.yaml * Update recipes/r-mytai/meta.yaml * Update recipes/r-mytai/meta.yaml * Add dependencies * Update_dependencies * add build.sh --------- Co-authored-by: Björn Grüning Co-authored-by: Bjoern Gruening --- recipes/r-mytai/build.sh | 7 ++++ recipes/r-mytai/meta.yaml | 81 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 recipes/r-mytai/build.sh create mode 100644 recipes/r-mytai/meta.yaml diff --git a/recipes/r-mytai/build.sh b/recipes/r-mytai/build.sh new file mode 100644 index 0000000000000..e8fdcfec9c6d1 --- /dev/null +++ b/recipes/r-mytai/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash +export DISABLE_AUTOBREW=1 + +mv DESCRIPTION DESCRIPTION.old +grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION +# shellcheck disable=SC2086 +${R} CMD INSTALL --build . ${R_ARGS} diff --git a/recipes/r-mytai/meta.yaml b/recipes/r-mytai/meta.yaml new file mode 100644 index 0000000000000..bcec0967095a4 --- /dev/null +++ b/recipes/r-mytai/meta.yaml @@ -0,0 +1,81 @@ +{% set name = "mytai" %} +{% set version = "0.9.3" %} + +package: + name: r-{{ name }} + version: '{{ version }}' + +source: + url: https://cran.r-project.org/src/contrib/myTAI_{{ version }}.tar.gz + sha256: 9dc0ed24dd75f763f909ecf763d873a2242640f49699e2e24739e2cf77d6a639 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - cross-r-base {{ r_base }} # [build_platform != target_platform] + - autoconf # [unix] + - "{{ compiler('c') }}" # [unix] + - "{{ compiler('m2w64_c') }}" # [win] + - "{{ compiler('cxx') }}" # [unix] + - "{{ compiler('m2w64_cxx') }}" # [win] + - posix # [win] + host: + - r-RColorBrewer >=1.1_2 + - r-Rcpp >=0.12.0 + - r-base >=3.1.1 + - r-doParallel >=1.0.8 + - r-dplyr >=0.3.0 + - bioconductor-edger + - r-fitdistrplus >=1.0_2 + - r-foreach >=1.4.2 + - r-ggplot2 >=1.0.1 + - r-gridExtra + - r-nortest >=1.0_2 + - r-readr >=0.2.2 + - r-reshape2 >=1.4.1 + - r-scales + - r-taxize >=0.6.0 + - r-tibble + - r-r.utils >=2.12.2 + - r-rcpparmadillo + - r-textshaping + - harfbuzz + - fribidi + run: + - r-RColorBrewer >=1.1_2 + - r-Rcpp >=0.12.0 + - r-base >=3.1.1 + - r-doParallel >=1.0.8 + - r-dplyr >=0.3.0 + - bioconductor-edger + - r-fitdistrplus >=1.0_2 + - r-foreach >=1.4.2 + - r-ggplot2 >=1.0.1 + - r-gridExtra + - r-nortest >=1.0_2 + - r-readr >=0.2.2 + - r-reshape2 >=1.4.1 + - r-scales + - r-taxize >=0.6.0 + - r-tibble + - r-r.utils >=2.12.2 + - r-rcpparmadillo + - r-textshaping +test: + commands: + - $R -e "library('myTAI')" # [not win] + +about: + home: https://github.com/drostlab/myTAI + summary: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2017) ). The aim of this tool is to provide a transcriptome analysis environment to quantify the average evolutionary age of genes contributing to a transcriptome of interest (Drost et al. (2016) ). + license: GPLv3 + license_family: GPL + +extra: + recipe-maintainers: + - gallardoalba From df6c7b59d13bcd03693c2b9cea6deb0526ff4a85 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 20:04:34 -0600 Subject: [PATCH 043/101] Update perl-http-date to 6.06 (#41874) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update perl-http-date to 6.06 * Update meta.yaml --------- Co-authored-by: Björn Grüning --- recipes/perl-http-date/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/perl-http-date/meta.yaml b/recipes/perl-http-date/meta.yaml index fa7ecea0268ae..158b9fd938aa4 100644 --- a/recipes/perl-http-date/meta.yaml +++ b/recipes/perl-http-date/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-http-date" %} -{% set version = "6.05" %} -{% set sha256 = "365d6294dfbd37ebc51def8b65b81eb79b3934ecbc95a2ec2d4d827efe6a922b" %} +{% set version = "6.06" %} +{% set sha256 = "7b685191c6acc3e773d1fc02c95ee1f9fae94f77783175f5e78c181cc92d2b52" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/O/OA/OALDERS/HTTP-Date-6.05.tar.gz + url: https://cpan.metacpan.org/authors/id/O/OA/OALDERS/HTTP-Date-6.06.tar.gz sha256: {{ sha256 }} build: @@ -23,7 +23,6 @@ requirements: - perl-extutils-makemaker - perl-file-spec - perl-io-handle - - perl-test - perl-test-more run: - perl From 032977aed9bcf6941284034e443b234e36af62e5 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 6 Jul 2023 21:40:36 -0500 Subject: [PATCH 044/101] Update vcflib to 1.0.9 (#41837) * Update vcflib to 1.0.9 * add make build dep * add python run dep * skip building on macOS * try building on macOS * try c++11 on osx * add ENABLE_CXX17_REMOVED_FEATURES * add D_LIBCPP_DISABLE_AVAILABILITY * edit -stdlib= * try without -stdlib=libc++ * skip building on macOS --- recipes/vcflib/build.sh | 67 +++++++++++++------------- recipes/vcflib/meta.yaml | 48 ++++++++++++------- recipes/vcflib/pkg-config.patch | 6 +-- recipes/vcflib/shared_lib.patch | 83 +++++++++++++++++++++++---------- recipes/vcflib/shared_ssw.patch | 17 ------- recipes/vcflib/tabix.patch | 17 +++++++ 6 files changed, 146 insertions(+), 92 deletions(-) delete mode 100644 recipes/vcflib/shared_ssw.patch create mode 100644 recipes/vcflib/tabix.patch diff --git a/recipes/vcflib/build.sh b/recipes/vcflib/build.sh index f3251168db95d..508ad993694d4 100644 --- a/recipes/vcflib/build.sh +++ b/recipes/vcflib/build.sh @@ -1,47 +1,50 @@ #!/bin/bash set -ex -export LDFLAGS="${LDFLAGS} -L$PREFIX/lib -lhts -ltabixpp -lpthread -lz -lm -llzma -lbz2" -export INCLUDES="-I . -Ihtslib -I$PREFIX/include -Itabixpp -I\$(INC_DIR) -L." -export LIBPATH="-L. -Lhtslib -L$PREFIX/lib -Ltabixpp" -export CXXFLAGS="${CXXFLAGS} -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x" +if [ `uname` == Darwin ]; then + echo $(pwd)/zig-macos-x86_64-* + export PATH="$(pwd)/zig-macos-x86_64-0.10.1:${PATH}" + else + echo $(pwd)/zig-linux-x86_64-* + export PATH="$(pwd)/zig-linux-x86_64-0.10.1:${PATH}" +fi + +export INCLUDES="-I${PREFIX}/include -I. -Ihtslib -Itabixpp -I\$(INC_DIR)" +export LIBPATH="-L${PREFIX}/lib -L. -Lhtslib -Ltabixpp" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib -lhts -ltabixpp -lpthread -lz -lm -llzma -lbz2 -fopenmp" +export CXXFLAGS="${CXXFLAGS} -O3 -D_FILE_OFFSET_BITS=64" -sed -i.bak 's/CFFFLAGS:= -O3/CFFFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -std=c++0x/' smithwaterman/Makefile -sed -i.bak 's/CFLAGS/CXXFLAGS/g' smithwaterman/Makefile +sed -i.bak 's/CFFFLAGS:= -O3/CFFFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -std=c++0x/' contrib/smithwaterman/Makefile +sed -i.bak 's/CFLAGS/CXXFLAGS/g' contrib/smithwaterman/Makefile -sed -i.bak 's/$=3 - - cmake - - pkg-config host: + - libgomp # [linux] + - llvm-openmp # [osx] + - zlib - htslib - tabixpp + - pkg-config + - wfa2-lib run: - python >=3 - - zlib + - perl - htslib - tabixpp + - eigen + - jsoncpp + - wfa2-lib test: commands: - - vcfallelicprimitives -h - - vcffirstheader < /dev/null - - vcfsort < /dev/null - - vcfrandom | grep 'fileformat=VCF' + - "vcfwave -h" + - "vcffirstheader < /dev/null" + - "vcfsort < /dev/null" about: home: https://github.com/vcflib/vcflib @@ -48,4 +64,4 @@ about: extra: identifiers: - biotools:vcflib - - doi:10.1101/023754 + - doi:10.1371/journal.pcbi.1009123 diff --git a/recipes/vcflib/pkg-config.patch b/recipes/vcflib/pkg-config.patch index 10ffa242b87c6..ae58978242cc2 100644 --- a/recipes/vcflib/pkg-config.patch +++ b/recipes/vcflib/pkg-config.patch @@ -1,8 +1,8 @@ Author: Andreas Tille modified for bioconda by Jon Puritz Description: Add pkg-config file to simplify building of freebayes Forwarded: not-needed ---- /dev/null -+++ libvcflib/libvcflib.pc +--- a/dev/null ++++ b/libvcflib/libvcflib.pc @@ -0,0 +1,12 @@ +prefix=/usr +exec_prefix=${prefix} @@ -11,7 +11,7 @@ Forwarded: not-needed + +Name: libvcflib +Version: 1.0 -+Requires: ++Requires: +Description: C++ library for parsing and manipulating VCF files +Libs: -L${libdir} -lvcflib +Cflags: -I${includedir} diff --git a/recipes/vcflib/shared_lib.patch b/recipes/vcflib/shared_lib.patch index bbb040a7ba6cc..aa04f6127490e 100644 --- a/recipes/vcflib/shared_lib.patch +++ b/recipes/vcflib/shared_lib.patch @@ -1,41 +1,76 @@ -Description: Build shared lib with bioconda's htslib and tabixpp - The upstream repo includes htslib as a submodule that gets - built with the tabixpp code. This patch changes this to use - bioconda's shared libhts from the archive. - Also builds a shared library instead of a static one. -Author: Andreas Tille modified for bioconda by Jon Puritz jpuritz@gmail.com ---- vcflib/CMakeLists.txt -+++ vcflib/CMakeLists.txt -@@ -74,7 +74,7 @@ - fastahack/*.h* - filevercmp/*.h*) - +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 088605d..15e52a5 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -76,8 +76,8 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release) + endif() + + if ((${CMAKE_BUILD_TYPE} MATCHES Release) OR (${CMAKE_BUILD_TYPE} MATCHES RelWithDebInfo)) +- set (CMAKE_C_FLAGS "${OpenMP_C_FLAGS} ${EXTRA_FLAGS}") +- set (CMAKE_CXX_FLAGS "${OpenMP_CXX_FLAGS} ${EXTRA_FLAGS}") ++ set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${EXTRA_FLAGS}") ++ set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${EXTRA_FLAGS}") + endif () + + if (${CMAKE_BUILD_TYPE} MATCHES "Debug") +@@ -116,12 +116,22 @@ include_directories(contrib/multichoose) + include_directories(contrib/filevercmp) + include_directories(contrib/c-progress-bar) + +-if(NOT HTSLIB_FOUND) ++if(HTSLIB_FOUND) ++ list(JOIN HTSLIB_CFLAGS " " HTSLIB_CFLAGS_STRING) ++ set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${HTSLIB_CFLAGS_STRING}") ++ set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${HTSLIB_CFLAGS_STRING}") ++else(HTSLIB_FOUND) ++ message(STATUS "Using included htslib") + set(HTSLIB_LOCAL contrib/tabixpp/htslib) +- set(TABIX_FOUND OFF) # also build tabixpp if htslib is missing ++ set(TABIXPP_FOUND OFF) # also build tabixpp if htslib is missing + endif() + +-if (NOT TABIX_FOUND) ++if (TABIXPP_FOUND) ++ list(JOIN TABIXPP_CFLAGS " " TABIXPP_CFLAGS_STRING) ++ set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${TABIXPP_CFLAGS_STRING}") ++ set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TABIXPP_CFLAGS_STRING}") ++else(TABIXPP_FOUND) ++ message(STATUS "Using included tabixpp") + set(TABIXPP_LOCAL contrib/tabixpp) + include_directories(contrib/tabixpp) + set(tabixpp_SOURCE +@@ -173,10 +183,14 @@ if (TABIXPP_LOCAL) # add the tabixpp source file + list(APPEND vcflib_SOURCE ${tabixpp_SOURCE}) + endif() + -add_library(vcflib STATIC +add_library(vcflib SHARED - src/Variant.h - src/split.h - src/pdflib.hpp -@@ -100,6 +100,12 @@ - filevercmp/filevercmp.c + ${vcflib_SOURCE} ) - -+target_link_libraries(vcflib + ++target_link_libraries(vcflib PUBLIC + tabixpp + ) -+ -+ + set(BINS vcfecho dumpContigsFromHeader -@@ -191,6 +197,10 @@ +@@ -309,6 +323,10 @@ set(SCRIPTS file (STRINGS "VERSION" BUILD_NUMBER) add_definitions(-DVCFLIB_VERSION="${BUILD_NUMBER}") add_definitions(-DVERSION="${BUILD_NUMBER}") +string(REGEX MATCH "^[0-9]+" MAJOR_BUILD_NUMBER ${BUILD_NUMBER}) +set_target_properties(vcflib PROPERTIES -+ SOVERSION ${MAJOR_BUILD_NUMBER} ++ SOVERSION ${MAJOR_BUILD_NUMBER} + ) - + # ---- Build htslib # +@@ -359,6 +377,7 @@ if (HTSLIB_LOCAL) + endif(HTSLIB_LOCAL) + + if(WFA_GITMODULE) ++ message(STATUS "Using included libwfa") + set(WFA_INCLUDE_DIRS ${WFA_LOCAL}) + add_subdirectory(${WFA_LOCAL} EXCLUDE_FROM_ALL) + set(WFALIB wfa2) # pick up the wfa2 lib target from the included CMakeLists.txt diff --git a/recipes/vcflib/shared_ssw.patch b/recipes/vcflib/shared_ssw.patch deleted file mode 100644 index ef34be41bcb81..0000000000000 --- a/recipes/vcflib/shared_ssw.patch +++ /dev/null @@ -1,17 +0,0 @@ -Description: Build shared lib with bioconda's htslib, tabixpp, and libssw - The upstream repo includes htslib as a submodule that gets - built with the tabixpp code. This patch changes this to use - bioconda's shared libhts from the archive. - Also builds a shared library instead of a static one. -Author: Andreas Tille modified for bioconda by Jon Puritz jpuritz@gmail.com ---- vcflib/src/Variant.h -+++ vcflib/src/Variant.h -@@ -28,7 +28,7 @@ - #include "join.h" - #include - #include "SmithWatermanGotoh.h" --#include "ssw_cpp.hpp" -+#include - #include "convert.h" - #include "multichoose.h" - #include diff --git a/recipes/vcflib/tabix.patch b/recipes/vcflib/tabix.patch new file mode 100644 index 0000000000000..cd25f54e22f24 --- /dev/null +++ b/recipes/vcflib/tabix.patch @@ -0,0 +1,17 @@ +--- a/contrib/tabixpp/tabix.hpp ++++ b/contrib/tabixpp/tabix.hpp +@@ -3,10 +3,10 @@ + #include + #include + #include +-#include "htslib/bgzf.h" +-#include "htslib/tbx.h" +-#include "htslib/kseq.h" +-#include "htslib/hfile.h" ++#include "htslib/htslib/bgzf.h" ++#include "htslib/htslib/tbx.h" ++#include "htslib/htslib/kseq.h" ++#include "htslib/htslib/hfile.h" + #include + #include + #include From 9ad73d3db4051360be45eabe90506846222584b9 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Fri, 7 Jul 2023 05:08:51 +0000 Subject: [PATCH 045/101] Added pandas dependency to matchms (#41875) --- recipes/matchms/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 99e85e308c61f..1eeb3285291ad 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 9ef706361b885f8c23e14b470adb3a18fc0b156a0a243b70de8ec998a41e05ba build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . -vv" noarch: python @@ -35,6 +35,7 @@ requirements: - sparsestack >=0.4.1 - tqdm - pillow =9.5 + - pandas test: From e789ceab5d7b340a6c11c52c705aa4a400cbda1f Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 7 Jul 2023 00:11:00 -0500 Subject: [PATCH 046/101] Update svim to 2.0.0 (#41876) --- recipes/svim/meta.yaml | 44 +++++++++++++++++++++++++++--------------- 1 file changed, 28 insertions(+), 16 deletions(-) diff --git a/recipes/svim/meta.yaml b/recipes/svim/meta.yaml index 32553b34153ab..0dee03e7271f8 100644 --- a/recipes/svim/meta.yaml +++ b/recipes/svim/meta.yaml @@ -1,41 +1,53 @@ -{% set version = "1.4.2" %} +{% set name = "SVIM" %} +{% set version = "2.0.0" %} +{% set sha256 = "1be9cfb84e420858b9e08fc3664b8d16d76bd2f241e6a87d876d9292d66ea1a3" %} package: - name: svim - version: '{{ version }}' + name: {{ name|lower }} + version: {{ version }} source: - url: https://github.com/eldariont/svim/archive/v{{ version }}.tar.gz - sha256: 790a51b30e80a0932ac95fc9c9626b2913907110b8bbc9e688fa37fc8ce32ab2 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/svim-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vv requirements: host: - - python >=3.6 + - python >=3.8 - pip run: - - python >=3.6 - - pysam >=0.15 + - python >=3.8 + - pysam >=0.15.2 - numpy - scipy - - matplotlib-base + - matplotlib-base >=3.3.0 + - python-edlib + - pyspoa >=0.0.6 + - py-cpuinfo >=7.0.0 - networkx - ngmlr - minimap2 - samtools -build: - number: 0 - noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv" - test: commands: - svim -h about: - home: 'https://github.com/eldariont/svim' + home: 'https://pypi.org/project/svim/' + summary: 'SVIM is a structural variant caller for long reads.' license: GPL-3.0 license_family: GPL license_file: LICENSE - summary: SVIM is a structural variant caller for long reads. + doc_url: 'https://github.com/eldariont/svim/wiki' + dev_url: 'https://github.com/eldariont/svim' +extra: + identifiers: + - doi:10.1093/bioinformatics/btz041 + recipe-maintainers: + - mencian From 59a23e244c6da5f08b4486237b07ffdef302ecdb Mon Sep 17 00:00:00 2001 From: Mike Tisza Date: Fri, 7 Jul 2023 00:11:28 -0500 Subject: [PATCH 047/101] Update esviritu to 0.2.3 (#41849) * Update meta.yaml * removing noarch from meta.yaml * returned to noarch python --- recipes/esviritu/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/esviritu/meta.yaml b/recipes/esviritu/meta.yaml index de8953958068b..0d562fbde46ab 100644 --- a/recipes/esviritu/meta.yaml +++ b/recipes/esviritu/meta.yaml @@ -1,5 +1,5 @@ {% set name = "esviritu" %} -{% set version = "0.2.2" %} +{% set version = "0.2.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/cmmr/{{ name }}/archive/v{{ version }}.tar.gz" - sha256: d647899d1395b77e1d4f894ed317b11f0340ab3e695daaeaacd76e665fd1cde8 + sha256: 19c0afbb59097f81ada768a2c55a0915678ebaf2f843589beb962ebf8522be31 build: number: 0 @@ -52,6 +52,7 @@ requirements: - r-readxl - r-lubridate - r-stringr + - biopython test: commands: From 5e25015a20d88d874bf1c1d4d35312b19a68b660 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Fri, 7 Jul 2023 09:59:19 +0200 Subject: [PATCH 048/101] [pmx_biobb] update 4.1.3 (#41857) * [pmx_biobb] update 4.1.3 * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/pmx_biobb/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/pmx_biobb/meta.yaml b/recipes/pmx_biobb/meta.yaml index c711e8d8d62ec..d85b1bbd42319 100644 --- a/recipes/pmx_biobb/meta.yaml +++ b/recipes/pmx_biobb/meta.yaml @@ -1,8 +1,8 @@ {% set name = "pmx_biobb" %} -{% set version = "4.1.2" %} +{% set version = "4.1.3" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "11a2ec951c376f51990c9b2c08f4112122a1e538076e9fe6e90cc0dbd4e5e856" %} +{% set hash_value = "87da97728646c871031f46ca05395c7b50cbb1f6e5637dc3a39b4cbf72f3cf58" %} package: name: '{{ name|lower }}' @@ -13,7 +13,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 2 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" @@ -30,6 +30,8 @@ requirements: - matplotlib-base - rdkit run: + - boost-cpp + - cxx-compiler - python - scipy - matplotlib-base From 9f1a10c42f91b1d54e23b2793ef9219ccaad2a21 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 7 Jul 2023 02:36:29 -0600 Subject: [PATCH 049/101] Update leviosam2 to 0.4.0 (#41839) * Update leviosam2 to 0.4.0 * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/leviosam2/meta.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/recipes/leviosam2/meta.yaml b/recipes/leviosam2/meta.yaml index 7ae5ef0425330..c327ca3da988b 100644 --- a/recipes/leviosam2/meta.yaml +++ b/recipes/leviosam2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.0" %} +{% set version = "0.4.0" %} package: name: leviosam2 @@ -6,10 +6,10 @@ package: source: url: https://github.com/milkschen/leviosam2/archive/refs/tags/v{{ version }}.tar.gz - sha256: b54301a0607df84679cd38b1eeed932cfd856dda48e5fd7c99430e80a5237c30 + sha256: 2ba4c2cf99ae2913673a20a824e60d5bee497ce0121f7a0bc3e1d9ae4c503092 build: - number: 2 + number: 0 requirements: build: @@ -17,10 +17,11 @@ requirements: - cmake - make host: - - htslib + - htslib >=1.11 - sdsl-lite >=2.1.1 run: - - htslib + - python >=3.6 + - htslib >=1.11 - sdsl-lite >=2.1.1 - zlib >=1.2.11,<1.3.0a0 From ca04772f73d258c40e7405fe8382acb3abd41515 Mon Sep 17 00:00:00 2001 From: danpal96 Date: Fri, 7 Jul 2023 05:53:09 -0400 Subject: [PATCH 050/101] added curl requirement to kaiju (#41051) Co-authored-by: Daniel Esteban Palma Igor Co-authored-by: Devon Ryan Co-authored-by: Brandon Seah --- recipes/kaiju/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/kaiju/meta.yaml b/recipes/kaiju/meta.yaml index 26fe2085f070a..e6eecd026bb1f 100644 --- a/recipes/kaiju/meta.yaml +++ b/recipes/kaiju/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 58d922358dfa4a608be888ec5c9e615b45b1e4be50615429183b0c5355e89c78 build: - number: 2 + number: 3 no_link: - bin/kaiju-makedb.sh @@ -25,6 +25,7 @@ requirements: - wget - zlib - python + - curl test: commands: From 833048c6f29224bbf8ae97472a9a27bd5f416522 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 7 Jul 2023 03:54:43 -0600 Subject: [PATCH 051/101] Update hopla to 1.2.1 (#41877) * Update hopla to 1.2.1 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/hopla/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/hopla/meta.yaml b/recipes/hopla/meta.yaml index 6bc1b7934f9cc..c628b8c8f198e 100644 --- a/recipes/hopla/meta.yaml +++ b/recipes/hopla/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.2.0" %} -{% set hash = "a0029b5d5588d6ad484ed6c7d31d74aa3e5cc2a8b88d144c71e91e7671c213f9" %} +{% set version = "1.2.1" %} +{% set hash = "ca41edf6402c5b5219959d29d922f5a1e812882f9c912f9903944b38d2cf685c" %} package: name: hopla @@ -16,7 +16,7 @@ build: requirements: run: - r-base - - r-vcfr >=1.8.0 + - r-vcfr >=1.12.0 - r-data.table >=1.13.2 - r-rcolorbrewer >=1.1_2 - r-kinship2 >=1.8.5 @@ -35,5 +35,6 @@ test: about: home: https://github.com/CenterForMedicalGeneticsGhent/Hopla license: MIT + license_family: MIT license_file: LICENSE summary: "Hopla enables classic genomic single, duo, trio, etc., analysis, by studying a single (multisample) vcf-file" From 84b9b880f181cd9c977b21aa15b1af8a872bf576 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Fri, 7 Jul 2023 12:12:29 +0200 Subject: [PATCH 052/101] Update meta.yaml to create py3.7 version (#41878) --- recipes/pmx_biobb/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pmx_biobb/meta.yaml b/recipes/pmx_biobb/meta.yaml index d85b1bbd42319..231ea0b39d417 100644 --- a/recipes/pmx_biobb/meta.yaml +++ b/recipes/pmx_biobb/meta.yaml @@ -13,7 +13,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" @@ -24,7 +24,7 @@ requirements: - {{ compiler('fortran') }} - make host: - - python + - python =3.7 - setuptools - scipy - matplotlib-base @@ -32,7 +32,7 @@ requirements: run: - boost-cpp - cxx-compiler - - python + - python =3.7 - scipy - matplotlib-base - rdkit From 1a061ffee2fa70839dccc8cfcfca3c93f56097e8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 7 Jul 2023 04:42:52 -0600 Subject: [PATCH 053/101] Update icount-mini to 3.0.0 (#41879) * Update icount-mini to 3.0.0 * Package license file --------- Co-authored-by: Christian Brueffer --- recipes/icount-mini/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/icount-mini/meta.yaml b/recipes/icount-mini/meta.yaml index 04da00261cd9c..6c14dfa4193ed 100644 --- a/recipes/icount-mini/meta.yaml +++ b/recipes/icount-mini/meta.yaml @@ -1,5 +1,5 @@ {% set name = "iCount-Mini" %} -{% set version = "2.0.3" %} +{% set version = "3.0.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: eabda13cef86833eb9d3ce1e3edd3d99759149056f328f70aa0fbba1312c0107 + sha256: a6c62b0b7dc0f0752ab693041edfab6dfec2510c5114e28ee8688dfc78a0a7f4 build: number: 0 @@ -50,6 +50,7 @@ about: home: "https://github.com/ulelab/iCount-Mini" license: MIT license_family: MIT + license_file: LICENSE summary: "Computational pipeline for analysis of iCLIP data" extra: From b3891dae30f486e294099ef3a3db7c078195ab49 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?= Date: Fri, 7 Jul 2023 13:47:58 +0200 Subject: [PATCH 054/101] Update blast: include *_vdb (#41861) * Update blast: include *_vdb * Add ncbi-vdb as deps and fix configure setting --- recipes/blast/build.sh | 5 +++-- recipes/blast/meta.yaml | 6 +++++- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/recipes/blast/build.sh b/recipes/blast/build.sh index c38b65bbef550..6042e111ee762 100644 --- a/recipes/blast/build.sh +++ b/recipes/blast/build.sh @@ -71,7 +71,7 @@ if [[ $(uname) = Linux ]] ; then --without-debug \ --with-experimental=Int8GI \ --with-strip \ - --without-vdb \ + --with-vdb=$PREFIX \ --with-z=$PREFIX \ --with-bz2=$PREFIX \ --without-krb5 \ @@ -90,7 +90,7 @@ else --without-debug \ --with-experimental=Int8GI \ --with-strip \ - --without-vdb \ + --with-vdb=$PREFIX \ --with-z=$PREFIX \ --with-bz2=$PREFIX \ --without-krb5 \ @@ -106,6 +106,7 @@ apps="$apps rpsblast.exe rpstblastn.exe makembindex.exe segmasker.exe" apps="$apps dustmasker.exe windowmasker.exe deltablast.exe makeblastdb.exe" apps="$apps blastdbcmd.exe blastdb_aliastool.exe convert2blastmask.exe" apps="$apps blastdbcheck.exe makeprofiledb.exe blast_formatter.exe rpsbproc.exe" +apps="$apps blastn_vdb.exe tblastn_vdb.exe" cd ReleaseMT # The "datatool" binary needs the libs at build time, create diff --git a/recipes/blast/meta.yaml b/recipes/blast/meta.yaml index cee0c51bbf906..56cab302b9316 100644 --- a/recipes/blast/meta.yaml +++ b/recipes/blast/meta.yaml @@ -24,7 +24,7 @@ source: - normbase.patch build: - number: 1 + number: 2 requirements: build: @@ -36,6 +36,7 @@ requirements: - bzip2 - pcre - entrez-direct + - ncbi-vdb - curl run: - zlib @@ -46,6 +47,7 @@ requirements: - perl-archive-tar - perl-json - entrez-direct + - ncbi-vdb - curl test: @@ -61,6 +63,7 @@ test: - blastdbcheck -version > /dev/null - blastdbcmd -version > /dev/null - blastn -version > /dev/null + - blastn_vdb -version > /dev/null - blastp -version > /dev/null - blastx -version > /dev/null - convert2blastmask -version > /dev/null @@ -73,6 +76,7 @@ test: - rpsbproc -version > /dev/null - segmasker -version > /dev/null - tblastn -version > /dev/null + - tblastn_vdb -version > /dev/null - tblastx -version > /dev/null - windowmasker -version > /dev/null - update_blastdb.pl --version > /dev/null From a60313950a774d9453d48d6d7f5384469b15b840 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Fri, 7 Jul 2023 14:15:56 +0200 Subject: [PATCH 055/101] [biobb_pmx] update 4.0.0 (#41882) * [biobb_pmx] update 4.0.0 * Update meta.yaml --- recipes/biobb_pmx/meta.yaml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/recipes/biobb_pmx/meta.yaml b/recipes/biobb_pmx/meta.yaml index 0f669584b0258..7163a4519a56e 100644 --- a/recipes/biobb_pmx/meta.yaml +++ b/recipes/biobb_pmx/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biobb_pmx" %} -{% set version = "3.8.1" %} +{% set version = "4.0.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 20fcb45053af24d5f68d2be2926281dcdd28c2c20b9cbe510161d8b101c845b1 + sha256: 0cd175a08b6d861d5ddc3c7b231eb92571649f8eadcc54936000c42930cc7792 build: @@ -20,16 +20,16 @@ requirements: host: - python >=3.7 - setuptools - - biobb_common ==3.8.1 - - pmx_biobb ==1.0.0 + - biobb_common ==4.0.0 + - pmx_biobb ==4.1.3 run: - python >=3.7 - - biobb_common ==3.8.1 - - pmx_biobb ==1.0.0 + - biobb_common ==4.0.0 + - pmx_biobb ==4.1.3 test: imports: - biobb_pmx - - biobb_pmx.pmx + - biobb_pmx.pmxbiobb about: home: https://github.com/bioexcel/biobb_pmx From c4cdc6617219fb81a3b56db4116297d28127532e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 7 Jul 2023 07:45:05 -0600 Subject: [PATCH 056/101] Update upimapi to 1.12.0 (#41885) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update upimapi to 1.12.0 * Update meta.yaml Re-added pyyaml as dependency --------- Co-authored-by: João Sequeira --- recipes/upimapi/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/upimapi/meta.yaml b/recipes/upimapi/meta.yaml index 50c1775674137..1a7bab190209b 100644 --- a/recipes/upimapi/meta.yaml +++ b/recipes/upimapi/meta.yaml @@ -1,6 +1,6 @@ {% set name = "upimapi" %} -{% set version = "1.11.2" %} -{% set sha256 = "28e9db5276903c886eb8438a2c3510cdb8374fec69e3420085c618e0d4054f96" %} +{% set version = "1.12.0" %} +{% set sha256 = "a03f0ef46f2f124675be2d394bf03ef13abdf97556e413d08333499ef7c46d17" %} package: name: {{ name|lower }} @@ -27,6 +27,7 @@ requirements: - tqdm - requests - biopython + - pyyaml test: commands: From 48f10edc888fd6a8c4c176db77528199919387e0 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Fri, 7 Jul 2023 22:14:57 -0500 Subject: [PATCH 057/101] Update ucsc-bigwig tools to 448 and remove them from the blacklist (#41407) * Update ucsc-bigwig tools and remove them from the blacklist * revert to skipping OSX * revert to skipping OSX for -fatovcf * remove ignore_run_exports --- build-fail-blacklist | 5 - recipes/ucsc-bigwigsummary/include.patch | 26 ++-- recipes/ucsc-bigwigsummary/meta.yaml | 21 +-- recipes/ucsc-bigwigtobedgraph/include.patch | 26 ++-- recipes/ucsc-bigwigtobedgraph/meta.yaml | 21 +-- recipes/ucsc-bigwigtowig/include.patch | 26 ++-- recipes/ucsc-bigwigtowig/meta.yaml | 23 ++-- recipes/ucsc-fatovcf/build.sh | 16 +-- recipes/ucsc-fatovcf/inc.common.mk.v426.patch | 121 ------------------ recipes/ucsc-fatovcf/include.patch | 35 +++++ recipes/ucsc-fatovcf/meta.yaml | 16 ++- recipes/ucsc-hggcpercent/include.patch | 26 ++-- recipes/ucsc-hggcpercent/meta.yaml | 21 +-- 13 files changed, 166 insertions(+), 217 deletions(-) delete mode 100644 recipes/ucsc-fatovcf/inc.common.mk.v426.patch create mode 100644 recipes/ucsc-fatovcf/include.patch diff --git a/build-fail-blacklist b/build-fail-blacklist index 626793dbd0200..352da75279a7b 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -835,9 +835,6 @@ recipes/ucsc-bigwigcluster recipes/ucsc-bigwigcorrelate recipes/ucsc-bigwiginfo recipes/ucsc-bigwigmerge -recipes/ucsc-bigwigsummary -recipes/ucsc-bigwigtobedgraph -recipes/ucsc-bigwigtowig recipes/ucsc-blasttopsl recipes/ucsc-catdir recipes/ucsc-catuncomment @@ -889,7 +886,6 @@ recipes/ucsc-fastqstatsandsubsample recipes/ucsc-fastqtofa recipes/ucsc-fatofastq recipes/ucsc-fatotab -recipes/ucsc-fatovcf recipes/ucsc-fatrans recipes/ucsc-featurebits recipes/ucsc-fetchchromsizes @@ -911,7 +907,6 @@ recipes/ucsc-headrest recipes/ucsc-hgbbidblink recipes/ucsc-hgfakeagp recipes/ucsc-hgfindspec -recipes/ucsc-hggcpercent recipes/ucsc-hggoldgapgl recipes/ucsc-hgloadbed recipes/ucsc-hgloadchain diff --git a/recipes/ucsc-bigwigsummary/include.patch b/recipes/ucsc-bigwigsummary/include.patch index eb32b88d8f358..e9c8621194325 100644 --- a/recipes/ucsc-bigwigsummary/include.patch +++ b/recipes/ucsc-bigwigsummary/include.patch @@ -1,22 +1,30 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a +--- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 ++++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 @@ -1,4 +1,4 @@ --#!/usr/bin/env python2.7 -+#!/usr/bin/env python - - import logging, sys, optparse, string - from collections import defaultdict +-KENT_INC=-I../../../inc ++KENT_INC=-I../../../inc -I${PREFIX}/include + + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-bigwigsummary/meta.yaml b/recipes/ucsc-bigwigsummary/meta.yaml index a2667d5afbaf2..1f60c5321b8a9 100644 --- a/recipes/ucsc-bigwigsummary/meta.yaml +++ b/recipes/ucsc-bigwigsummary/meta.yaml @@ -1,39 +1,40 @@ {% set package = "ucsc-bigwigsummary" %} {% set program = "bigWigSummary" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "448" %} +{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %} package: - name: "{{ package }}" - version: "{{ version }}" + name: {{ package }} + version: {{ version }} source: - url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: "{{ sha256 }}" + url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz + sha256: {{ sha256 }} patches: - - "include.patch" + - include.patch build: + number: 0 skip: True # [osx] - number: 4 requirements: build: - make - {{ compiler('c') }} + - {{ compiler('cxx') }} + - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - openssl + - libopenssl-static - zlib - run: - libpng - libuuid - mysql-connector-c - openssl - - zlib test: commands: diff --git a/recipes/ucsc-bigwigtobedgraph/include.patch b/recipes/ucsc-bigwigtobedgraph/include.patch index eb32b88d8f358..e9c8621194325 100644 --- a/recipes/ucsc-bigwigtobedgraph/include.patch +++ b/recipes/ucsc-bigwigtobedgraph/include.patch @@ -1,22 +1,30 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a +--- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 ++++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 @@ -1,4 +1,4 @@ --#!/usr/bin/env python2.7 -+#!/usr/bin/env python - - import logging, sys, optparse, string - from collections import defaultdict +-KENT_INC=-I../../../inc ++KENT_INC=-I../../../inc -I${PREFIX}/include + + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-bigwigtobedgraph/meta.yaml b/recipes/ucsc-bigwigtobedgraph/meta.yaml index cd43e2f2b6345..ca9508fd1a62d 100644 --- a/recipes/ucsc-bigwigtobedgraph/meta.yaml +++ b/recipes/ucsc-bigwigtobedgraph/meta.yaml @@ -1,39 +1,40 @@ {% set package = "ucsc-bigwigtobedgraph" %} {% set program = "bigWigToBedGraph" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "448" %} +{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %} package: - name: "{{ package }}" - version: "{{ version }}" + name: {{ package }} + version: {{ version }} source: - url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: "{{ sha256 }}" + url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz + sha256: {{ sha256 }} patches: - - "include.patch" + - include.patch build: + number: 0 skip: True # [osx] - number: 7 requirements: build: - make - {{ compiler('c') }} + - {{ compiler('cxx') }} + - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - openssl + - libopenssl-static - zlib - run: - libpng - libuuid - mysql-connector-c - openssl - - zlib test: commands: diff --git a/recipes/ucsc-bigwigtowig/include.patch b/recipes/ucsc-bigwigtowig/include.patch index eb32b88d8f358..e9c8621194325 100644 --- a/recipes/ucsc-bigwigtowig/include.patch +++ b/recipes/ucsc-bigwigtowig/include.patch @@ -1,22 +1,30 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a +--- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 ++++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 @@ -1,4 +1,4 @@ --#!/usr/bin/env python2.7 -+#!/usr/bin/env python - - import logging, sys, optparse, string - from collections import defaultdict +-KENT_INC=-I../../../inc ++KENT_INC=-I../../../inc -I${PREFIX}/include + + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-bigwigtowig/meta.yaml b/recipes/ucsc-bigwigtowig/meta.yaml index 502e85152f9ac..72927f2fed2f3 100644 --- a/recipes/ucsc-bigwigtowig/meta.yaml +++ b/recipes/ucsc-bigwigtowig/meta.yaml @@ -1,39 +1,40 @@ {% set package = "ucsc-bigwigtowig" %} {% set program = "bigWigToWig" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "448" %} +{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %} package: - name: "{{ package }}" - version: "{{ version }}" + name: {{ package }} + version: {{ version }} source: - url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: "{{ sha256 }}" + url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz + sha256: {{ sha256 }} patches: - - "include.patch" + - include.patch build: + number: 0 skip: True # [osx] - number: 4 requirements: build: - make - {{ compiler('c') }} + - {{ compiler('cxx') }} + - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - openssl + - libopenssl-static - zlib - run: - libpng - libuuid - mysql-connector-c - openssl - - zlib test: commands: @@ -43,4 +44,4 @@ test: about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" - summary: "Convert bigWig to wig. This will keep more of the same structure of the" + summary: "Convert bigWig to wig. This will keep more of the same structure of the original wig than bigWigToBedGraph does, but still will break up large stepped sections into smaller ones." diff --git a/recipes/ucsc-fatovcf/build.sh b/recipes/ucsc-fatovcf/build.sh index 274cf0bfb40de..1074509ead921 100644 --- a/recipes/ucsc-fatovcf/build.sh +++ b/recipes/ucsc-fatovcf/build.sh @@ -1,20 +1,20 @@ #!/bin/bash -export CFLAGS="$CFLAGS -I$PREFIX/include" -export LDFLAGS="$LDFLAGS -L$PREFIX/lib" -export CPATH=${PREFIX}/include +export INCLUDE_PATH=${PREFIX}/include +export LIBRARY_PATH=${PREFIX}/lib +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -I${PREFIX}/include ${LDFLAGS}" export USE_HIC=0 -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=x86_64 export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -patch kent/src/inc/common.mk $RECIPE_DIR/inc.common.mk.v426.patch +mkdir -p "${BINDIR}" (cd kent/src/lib && make) (cd kent/src/htslib && make) (cd kent/src/jkOwnLib && make) (cd kent/src/hg/lib && make) (cd kent/src/hg/utils/faToVcf && make) -cp bin/faToVcf "$PREFIX/bin" -chmod +x "$PREFIX/bin/faToVcf" +cp bin/faToVcf "${PREFIX}/bin" +chmod +x "${PREFIX}/bin/faToVcf" diff --git a/recipes/ucsc-fatovcf/inc.common.mk.v426.patch b/recipes/ucsc-fatovcf/inc.common.mk.v426.patch deleted file mode 100644 index 65c8e942b32ab..0000000000000 --- a/recipes/ucsc-fatovcf/inc.common.mk.v426.patch +++ /dev/null @@ -1,121 +0,0 @@ -diff --git a/src/inc/common.mk b/src/inc/common.mk -index 1c6c0e93d9..0c3abb2ac7 100644 ---- a/src/inc/common.mk -+++ b/src/inc/common.mk -@@ -34,36 +34,41 @@ else - IS_HGWDEV = no - endif - --FREETYPECFLAGS = $(shell freetype-config --cflags 2> /dev/null) -- --# we use our static library on dev --ifeq (${IS_HGWDEV},no) -- ifeq (${FREETYPELIBS},) -- ifeq ($(UNAME_S),Darwin) -- ifneq ($(wildcard /usr/local/Cellar/freetype/2.11.0/lib/libfreetype.a),) -- ifneq ($(wildcard /usr/local/opt/bzip2/lib/libbz2.a),) -- FREETYPELIBS = /usr/local/Cellar/freetype/2.11.0/lib/libfreetype.a /usr/local/opt/bzip2/lib/libbz2.a -+# Skip freetype for conda build; not needed for utils, and the Mac build environment has -+# freetype installed but we don't want to use the system libraries because they can be -+# for a newer OSX version than the conda build target, and can be incompatible. -+ifneq (${CONDA_BUILD},1) -+ FREETYPECFLAGS = $(shell freetype-config --cflags 2> /dev/null) -+ -+ # we use our static library on dev -+ ifeq (${IS_HGWDEV},no) -+ ifeq (${FREETYPELIBS},) -+ ifeq ($(UNAME_S),Darwin) -+ ifneq ($(wildcard /usr/local/Cellar/freetype/2.11.0/lib/libfreetype.a),) -+ ifneq ($(wildcard /usr/local/opt/bzip2/lib/libbz2.a),) -+ FREETYPELIBS = /usr/local/Cellar/freetype/2.11.0/lib/libfreetype.a /usr/local/opt/bzip2/lib/libbz2.a -+ else -+ FREETYPELIBS = /usr/local/Cellar/freetype/2.11.0/lib/libfreetype.a -lbz2 -+ endif - else -- FREETYPELIBS = /usr/local/Cellar/freetype/2.11.0/lib/libfreetype.a -lbz2 -- endif -- else -- ifneq ($(wildcard /opt/local/lib/libfreetype.a),) -- FREETYPELIBS=/opt/local/lib/libfreetype.a /opt/local/lib/libbz2.a /opt/local/lib/libbrotlidec-static.a /opt/local/lib/libbrotlienc-static.a /opt/local/lib/libbrotlicommon-static.a -+ ifneq ($(wildcard /opt/local/lib/libfreetype.a),) -+ FREETYPELIBS=/opt/local/lib/libfreetype.a /opt/local/lib/libbz2.a /opt/local/lib/libbrotlidec-static.a /opt/local/lib/libbrotlienc-static.a /opt/local/lib/libbrotlicommon-static.a -+ endif - endif - endif -- endif -- ifeq (${FREETYPELIBS},) -- FREETYPELIBS = $(shell freetype-config --libs 2> /dev/null ) -+ ifeq (${FREETYPELIBS},) -+ FREETYPELIBS = $(shell freetype-config --libs 2> /dev/null ) -+ endif - endif - endif --endif - --ifneq (${FREETYPECFLAGS},) --FREETYPECFLAGS += -DUSE_FREETYPE --endif -+ ifneq (${FREETYPECFLAGS},) -+ FREETYPECFLAGS += -DUSE_FREETYPE -+ endif - --HG_INC += ${FREETYPECFLAGS} --L += ${FREETYPELIBS} -+ HG_INC += ${FREETYPECFLAGS} -+ L += ${FREETYPELIBS} -+endif - - ifeq (${IS_HGWDEV},yes) - FULLWARN = yes -@@ -138,28 +143,32 @@ ifeq (${IS_HGWDEV},yes) - L+=/hive/groups/browser/freetype/freetype-2.10.0/objs/.libs/libfreetype.a -lbz2 - L+=/usr/lib64/libssl.a /usr/lib64/libcrypto.a -lkrb5 -lk5crypto -ldl - else -- ifneq ($(wildcard /opt/local/lib/libssl.a),) -- L+=/opt/local/lib/libssl.a -+ ifeq (${CONDA_BUILD},1) -+ L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a - else -- ifneq ($(wildcard /usr/lib/x86_64-linux-gnu/libssl.a),) -- L+=/usr/lib/x86_64-linux-gnu/libssl.a -+ ifneq ($(wildcard /opt/local/lib/libssl.a),) -+ L+=/opt/local/lib/libssl.a - else -- ifneq ($(wildcard /usr/local/opt/openssl/lib/libssl.a),) -- L+=/usr/local/opt/openssl/lib/libssl.a -- else -- L+=-lssl -- endif -+ ifneq ($(wildcard /usr/lib/x86_64-linux-gnu/libssl.a),) -+ L+=/usr/lib/x86_64-linux-gnu/libssl.a -+ else -+ ifneq ($(wildcard /usr/local/opt/openssl/lib/libssl.a),) -+ L+=/usr/local/opt/openssl/lib/libssl.a -+ else -+ L+=-lssl -+ endif -+ endif - endif -- endif -- ifneq ($(wildcard /opt/local/lib/libcrypto.a),) -- L+=/opt/local/lib/libcrypto.a -- else -- ifneq ($(wildcard /usr/local/opt/openssl/lib/libcrypto.a),) -- L+=/usr/local/opt/openssl/lib/libcrypto.a -- else -- L+=-lcrypto -- endif -- endif -+ ifneq ($(wildcard /opt/local/lib/libcrypto.a),) -+ L+=/opt/local/lib/libcrypto.a -+ else -+ ifneq ($(wildcard /usr/local/opt/openssl/lib/libcrypto.a),) -+ L+=/usr/local/opt/openssl/lib/libcrypto.a -+ else -+ L+=-lcrypto -+ endif -+ endif -+ endif - endif - - # autodetect where libm is installed diff --git a/recipes/ucsc-fatovcf/include.patch b/recipes/ucsc-fatovcf/include.patch new file mode 100644 index 0000000000000..e9c8621194325 --- /dev/null +++ b/recipes/ucsc-fatovcf/include.patch @@ -0,0 +1,35 @@ +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +@@ -17,7 +17,7 @@ + endif + + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} +-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include + + # to check for Mac OSX Darwin specifics: + UNAME_S := $(shell uname -s) +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a +--- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 ++++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +@@ -1,4 +1,4 @@ +-KENT_INC=-I../../../inc ++KENT_INC=-I../../../inc -I${PREFIX}/include + + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + # expMatrixToBarchartBed + """ + Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. diff --git a/recipes/ucsc-fatovcf/meta.yaml b/recipes/ucsc-fatovcf/meta.yaml index 0f409f6c7469b..1d2de4903514d 100644 --- a/recipes/ucsc-fatovcf/meta.yaml +++ b/recipes/ucsc-fatovcf/meta.yaml @@ -1,24 +1,28 @@ {% set package = "ucsc-fatovcf" %} {% set program = "faToVcf" %} -{% set version = "426" %} -{% set sha256 = "b79d057adeac0c1c2997da3975c103d4b4bdf8ecdaf49a9d48ed091fc5ebf74a" %} +{% set version = "448" %} +{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %} package: - name: "{{ package }}" - version: "{{ version }}" + name: {{ package }} + version: {{ version }} source: - url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: "{{ sha256 }}" + url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz + sha256: {{ sha256 }} + patches: + - include.patch build: number: 0 + skip: True # [osx] requirements: build: - make - {{ compiler('c') }} - {{ compiler('cxx') }} + - binutils # [linux] host: - libpng - libuuid diff --git a/recipes/ucsc-hggcpercent/include.patch b/recipes/ucsc-hggcpercent/include.patch index eb32b88d8f358..e9c8621194325 100644 --- a/recipes/ucsc-hggcpercent/include.patch +++ b/recipes/ucsc-hggcpercent/include.patch @@ -1,22 +1,30 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 ++++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 +@@ -147,4 +147,4 @@ +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl ++ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl + else + ifneq ($(wildcard /opt/local/lib/libssl.a),) + L+=/opt/local/lib/libssl.a +--- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 ++++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 @@ -1,4 +1,4 @@ --#!/usr/bin/env python2.7 -+#!/usr/bin/env python - - import logging, sys, optparse, string - from collections import defaultdict +-KENT_INC=-I../../../inc ++KENT_INC=-I../../../inc -I${PREFIX}/include + + straw: straw.o cStraw.o + ld -r -o ../straw.o straw.o cStraw.o --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-hggcpercent/meta.yaml b/recipes/ucsc-hggcpercent/meta.yaml index ba1139116cd30..4b567ff8e2715 100644 --- a/recipes/ucsc-hggcpercent/meta.yaml +++ b/recipes/ucsc-hggcpercent/meta.yaml @@ -1,39 +1,40 @@ {% set package = "ucsc-hggcpercent" %} {% set program = "hgGcPercent" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "448" %} +{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %} package: - name: "{{ package }}" - version: "{{ version }}" + name: {{ package }} + version: {{ version }} source: - url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: "{{ sha256 }}" + url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz + sha256: {{ sha256 }} patches: - - "include.patch" + - include.patch build: + number: 0 skip: True # [osx] - number: 4 requirements: build: - make - {{ compiler('c') }} + - {{ compiler('cxx') }} + - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - openssl + - libopenssl-static - zlib - run: - libpng - libuuid - mysql-connector-c - openssl - - zlib test: commands: From 96d2ff0c304fc15e6662eb3f6a8d4ef9730a5698 Mon Sep 17 00:00:00 2001 From: Bede Constantinides <1007616+bede@users.noreply.github.com> Date: Sat, 8 Jul 2023 05:00:17 +0100 Subject: [PATCH 058/101] Add Hostile (#41889) * Add recipe for Hostile * Update meta.yml * add dependencies * clean up depends * Rename meta.yml to meta.yaml * Add python depends * fix typo * move flit dependency --------- Co-authored-by: Robert A. Petit III --- recipes/hostile/meta.yaml | 50 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 recipes/hostile/meta.yaml diff --git a/recipes/hostile/meta.yaml b/recipes/hostile/meta.yaml new file mode 100644 index 0000000000000..27facc3ec38bb --- /dev/null +++ b/recipes/hostile/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "0.0.2" %} + +package: + name: hostile + version: {{ version }} + +source: + url: https://pypi.io/packages/source/h/hostile/hostile-{{ version }}.tar.gz + sha256: 1e583b611deff299319852476d38102ac6fafb3f69fe46c2e7459c36e2d566aa + +build: + noarch: python + number: 0 + entry_points: + - hostile = hostile.cli:main + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" + +requirements: + host: + - pip + - python >=3.10 + - flit-core >=3.9.0 + run: + - bowtie2 >=2.5.1 + - defopt >=6.4.0 + - gawk >=5.1.0 + - httpx >=0.24.1 + - minimap2 >=2.26 + - platformdirs >=3.5.1 + - python >=3.10 + - samtools >=1.17 + - tqdm >=4.65.0 + +test: + imports: + - hostile + + commands: + - hostile --version + +about: + home: https://github.com/bede/hostile + license: MIT License + license_family: MIT + license_file: LICENSE + summary: 'Hostile: accurate host decontamination' + +extra: + identifiers: + - doi:10.1101/2023.07.04.547735 From a39c30f996d3c286ff393db1fbdf6dfc716bc90b Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sat, 8 Jul 2023 01:59:41 -0500 Subject: [PATCH 059/101] Update pxblat recipe and reset build number (#41895) * Update pxblat recipe and bump build number * reset build number to 0 --- recipes/pxblat/meta.yaml | 57 ++++++++++++++++++++++++++++++++++++++++ recipes/pxblat/meta.yml | 50 ----------------------------------- 2 files changed, 57 insertions(+), 50 deletions(-) create mode 100644 recipes/pxblat/meta.yaml delete mode 100644 recipes/pxblat/meta.yml diff --git a/recipes/pxblat/meta.yaml b/recipes/pxblat/meta.yaml new file mode 100644 index 0000000000000..720c3bc86664b --- /dev/null +++ b/recipes/pxblat/meta.yaml @@ -0,0 +1,57 @@ +{% set name = "PxBLAT" %} +{% set version = "0.2.0" %} +{% set sha256 = "22f7b66da9b0c799aeb84d74040ed3ab0eb96f5a15ebcbcbc3e67133668e9b96" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pxblat-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + skip: True # [py < 39] + script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vv + +requirements: + build: + - {{ compiler('cxx') }} + host: + - python + - pip + - pybind11 >2.9.1 + - poetry-core >=1.2.0 + - setuptools >=67.7.2 + - zlib + - htslib + - openssl + run: + - python + - loguru + - rich + - pysimdjson + - biopython + - typer + - deprecated + - mashumaro + - numpy >=1.24.3 + +test: + imports: + - pxblat + commands: + - pxblat -h + +about: + home: 'https://pypi.org/project/pxblat/' + summary: 'PxBLAT: An Efficient and Ergonomics Python Binding Library for BLAT.' + license: MIT + license_file: LICENSE + dev_url: 'https://github.com/cauliyang/pxblat' + doc_url: 'https://pxblat.readthedocs.io/en/latest/' + +extra: + recipe-maintainers: + - yangyangli diff --git a/recipes/pxblat/meta.yml b/recipes/pxblat/meta.yml deleted file mode 100644 index e488fdc729dab..0000000000000 --- a/recipes/pxblat/meta.yml +++ /dev/null @@ -1,50 +0,0 @@ -{% set name = "pxblat" %} -{% set version = "0.2.0" %} - -package: - name: "{{ name|lower }}" - version: "{{ version }}" - -source: - url: https://github.com/cauliyang/pxblat/archive/v{{ version }}.tar.gz - sha256: ac8132e9a33854963f42e027e7f2a5280ac516076b109cd07cacd26745a16c7b - -build: - number: 1 - skip: True #[py2k or win] - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv " - -requirements: - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - host: - - python >=3.9 - - pip - - pybind11 >=2.9.1 - - setuptools >=46.4 - - zlib - - htslib - - openssl - run: - - python >=3.9 - - zlib - - htslib - - openssl - -test: - imports: - - {{ name }} - commands: - - pxblat -h - -about: - home: https://github.com/cauliyang/pxblat - license: MIT - license_file: COPYING - summary: PxBLAT: An Efficient and Ergonomics Python Binding Library for BLAT. - doc_url: https://github.com/cauliyang/pxblat - -extra: - recipe-maintainers: - - yangyangli From 27d16d8ceb6b6dfd924077414e2a0d739df96d18 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 8 Jul 2023 01:00:12 -0600 Subject: [PATCH 060/101] Update vsearch to 2.23.0 (#41884) --- recipes/vsearch/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index 9482f8b5ac4b2..19b601ca2618a 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.22.1" %} -{% set sha256 = "c62bf69e7cc3d011a12e3b522ba8c0c91fb90deea782359e9569677d0c991778" %} +{% set version = "2.23.0" %} +{% set sha256 = "4686e35e1d8488ffedb4c6dd4de9b6eccc94f337d7b86e1759d932bce59c9b64" %} package: name: vsearch @@ -10,7 +10,7 @@ source: sha256: '{{ sha256 }}' build: - number: 2 + number: 0 requirements: build: From 34adcbef9579f13229167fbd8070feae37209ae9 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Sat, 8 Jul 2023 09:00:48 +0200 Subject: [PATCH 061/101] Remove outdated dependency restrictions for pangolin (#41880) Since v4.3 pangolin works again with the latest releases of all its dependencies. --- recipes/pangolin/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pangolin/meta.yaml b/recipes/pangolin/meta.yaml index f2187b9511f34..e35e53f64ba4c 100644 --- a/recipes/pangolin/meta.yaml +++ b/recipes/pangolin/meta.yaml @@ -9,7 +9,7 @@ source: sha256: daf13c111799943b05bc2c8eee8deb2316e1347ca8f40f0b40d22cdbcc72e3c1 build: - number: 0 + number: 1 noarch: python script: python -m pip install --no-deps --ignore-installed . @@ -21,12 +21,12 @@ requirements: - python >=3.7 - biopython ==1.74 - pandas >=1.0.1 - - tabulate ==0.8.10 + - tabulate - joblib >=0.11 - scikit-learn >=0.23.1 - pulp >=2 - minimap2 >=2.16 - - snakemake-minimal >=5.13,<=6.8.0 + - snakemake-minimal >=5.13 - gofasta - usher >=0.6.2 - ucsc-fatovcf >=426 From 6d838b6bb40ff3e047763c1bf984d8084ab0bc38 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sat, 8 Jul 2023 02:02:42 -0500 Subject: [PATCH 062/101] Update spoa to 4.0.8 (#41893) * Update spoa to 4.0.8 * edit cmake options --- recipes/spoa/build.sh | 27 +++++++++++++++++---------- recipes/spoa/meta.yaml | 33 +++++++++++++++++++++------------ 2 files changed, 38 insertions(+), 22 deletions(-) diff --git a/recipes/spoa/build.sh b/recipes/spoa/build.sh index 3ba42dc663cd5..9a3c2843d27e5 100644 --- a/recipes/spoa/build.sh +++ b/recipes/spoa/build.sh @@ -1,14 +1,21 @@ #!/bin/bash set -eoux pipefail -mkdir build -pushd build -cmake -DCMAKE_BUILD_TYPE=Release -Dspoa_build_executable=ON -Dspoa_optimize_for_portability=ON .. -make +export INCLUDES="-I{PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3" -mkdir -p ${PREFIX}/bin -mkdir -p ${PREFIX}/lib -mkdir -p ${PREFIX}/include -mv ../include/spoa ${PREFIX}/include/ -mv lib/libspoa.a ${PREFIX}/lib/ -mv bin/spoa ${PREFIX}/bin/ +cmake -S . -B build \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DCMAKE_BUILD_TYPE=Release \ + -DBUILD_SHARED_LIBS=ON \ + -Dspoa_install=ON \ + -Dspoa_build_exe=ON \ + -Dspoa_optimize_for_portability=ON \ + -Dspoa_use_simde=ON \ + -Dspoa_use_simde_openmp=ON \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" + +cmake --build build/ --target install -j 4 -v diff --git a/recipes/spoa/meta.yaml b/recipes/spoa/meta.yaml index e3b2b46b3ac4f..a7bd1400c5198 100644 --- a/recipes/spoa/meta.yaml +++ b/recipes/spoa/meta.yaml @@ -1,32 +1,41 @@ -{% set version = "4.0.7" %} +{% set name = "spoa" %} +{% set version = "4.0.8" %} +{% set sha256 = "3fc7e837b1052bd470924e37e0ed9531e7c839cd14b400573171d3d46d3ed9cd" %} package: - name: spoa + name: {{ name }} version: {{ version }} -build: - number: 5 - run_exports: - - {{ pin_subpackage('spoa', max_pin='x.x') }} - source: - url: https://github.com/rvaser/spoa/releases/download/{{ version }}/spoa-v{{ version }}.tar.gz - sha256: f7a8cd039e4aabea1481e123387fedaa8f87e55418a3649408a615f5c6b1b9a4 + url: https://github.com/rvaser/spoa/archive/refs/tags/{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 requirements: build: - - make - {{ compiler('cxx') }} + - make - cmake host: - zlib + - simde + - libgomp # [linux] + - llvm-openmp # [osx] + - cpu_features test: commands: - spoa --help about: - home: https://github.com/rvaser/spoa + home: 'https://github.com/rvaser/spoa' license: MIT license_file: LICENSE - summary: SIMD partial order alignment tool/library + summary: 'SIMD partial order alignment tool/library' + +extra: + identifiers: + - biotools:spoa + - doi:10.1101/gr.214270.116 From 484d2642cab837344f34e5a7fce37372df9128f2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 8 Jul 2023 03:23:36 -0600 Subject: [PATCH 063/101] Update python-nextflow to 0.6.1 (#41892) --- recipes/python-nextflow/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/python-nextflow/meta.yaml b/recipes/python-nextflow/meta.yaml index eda5c8d555be7..8349366ff562a 100644 --- a/recipes/python-nextflow/meta.yaml +++ b/recipes/python-nextflow/meta.yaml @@ -1,6 +1,6 @@ {% set name="python-nextflow" %} {% set repo="nextflow.py" %} -{% set version="0.6" %} +{% set version="0.6.1" %} package: @@ -14,7 +14,7 @@ build: source: url: https://github.com/goodwright/{{ repo }}/archive/v{{ version }}.tar.gz - sha256: 8981bb54a30006e08739319b368decb799eb9794c9914f802fefb48c6b43f7ff + sha256: b3dc57426f64e27ace26f9428a91be34cf1585ebd5a79334809680ede1c7d975 requirements: host: From 549f5603ffc61d7419ef0bd9cacaabe00342af93 Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Sat, 8 Jul 2023 12:46:41 +0200 Subject: [PATCH 064/101] Remove r-interpretmsspectrum, it has been migrated to conda-corge. (#41896) --- recipes/r-interpretmsspectrum/build.sh | 41 ----------------------- recipes/r-interpretmsspectrum/meta.yaml | 43 ------------------------- 2 files changed, 84 deletions(-) delete mode 100644 recipes/r-interpretmsspectrum/build.sh delete mode 100644 recipes/r-interpretmsspectrum/meta.yaml diff --git a/recipes/r-interpretmsspectrum/build.sh b/recipes/r-interpretmsspectrum/build.sh deleted file mode 100644 index 88ea7b44d4489..0000000000000 --- a/recipes/r-interpretmsspectrum/build.sh +++ /dev/null @@ -1,41 +0,0 @@ -#!/bin/bash - -set -o errexit -o pipefail - -if [[ ${target_platform} =~ linux.* ]] || [[ ${target_platform} == osx-64 ]]; then - export DISABLE_AUTOBREW=1 - mv DESCRIPTION DESCRIPTION.old - grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION - ${R} CMD INSTALL --build . -else - mkdir -p "${PREFIX}"/lib/R/library/InterpretMSSpectrum - mv ./* "${PREFIX}"/lib/R/library/InterpretMSSpectrum - - if [[ ${target_platform} == osx-64 ]]; then - pushd "${PREFIX}" - for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do - pushd "${libdir}" || exit 1 - while IFS= read -r -d '' SHARED_LIB - do - echo "fixing SHARED_LIB ${SHARED_LIB}" - install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "${PREFIX}"/lib/R/lib/libR.dylib "${SHARED_LIB}" || true - install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "${PREFIX}"/lib/R/lib/libR.dylib "${SHARED_LIB}" || true - install_name_tool -change /usr/local/clang4/lib/libomp.dylib "${PREFIX}"/lib/libomp.dylib "${SHARED_LIB}" || true - install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "${PREFIX}"/lib/libgfortran.3.dylib "${SHARED_LIB}" || true - install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "${PREFIX}"/lib/libquadmath.0.dylib "${SHARED_LIB}" || true - install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "${PREFIX}"/lib/libquadmath.0.dylib "${SHARED_LIB}" || true - install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "${PREFIX}"/lib/libgfortran.3.dylib "${SHARED_LIB}" || true - install_name_tool -change /usr/lib/libgcc_s.1.dylib "${PREFIX}"/lib/libgcc_s.1.dylib "${SHARED_LIB}" || true - install_name_tool -change /usr/lib/libiconv.2.dylib "${PREFIX}"/sysroot/usr/lib/libiconv.2.dylib "${SHARED_LIB}" || true - install_name_tool -change /usr/lib/libncurses.5.4.dylib "${PREFIX}"/sysroot/usr/lib/libncurses.5.4.dylib "${SHARED_LIB}" || true - install_name_tool -change /usr/lib/libicucore.A.dylib "${PREFIX}"/sysroot/usr/lib/libicucore.A.dylib "${SHARED_LIB}" || true - install_name_tool -change /usr/lib/libexpat.1.dylib "${PREFIX}"/lib/libexpat.1.dylib "${SHARED_LIB}" || true - install_name_tool -change /usr/lib/libcurl.4.dylib "${PREFIX}"/lib/libcurl.4.dylib "${SHARED_LIB}" || true - install_name_tool -change /usr/lib/libc++.1.dylib "${PREFIX}"/lib/libc++.1.dylib "${SHARED_LIB}" || true - install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "${PREFIX}"/lib/libc++.1.dylib "${SHARED_LIB}" || true - done < <(find . \( -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R" \) -print0) - popd - done - popd - fi -fi diff --git a/recipes/r-interpretmsspectrum/meta.yaml b/recipes/r-interpretmsspectrum/meta.yaml deleted file mode 100644 index 5547063e2a1f1..0000000000000 --- a/recipes/r-interpretmsspectrum/meta.yaml +++ /dev/null @@ -1,43 +0,0 @@ -{% set version = '1.3.3' %} - -package: - name: r-interpretmsspectrum - version: {{ version|replace("-", "_") }} - -source: - url: - - {{ cran_mirror }}/src/contrib/InterpretMSSpectrum_{{ version }}.tar.gz - - {{ cran_mirror }}/src/contrib/Archive/InterpretMSSpectrum/InterpretMSSpectrum_{{ version }}.tar.gz - sha256: 306a1541504088a05636f49e71a12d806f32fcaaa2d0622a58288452012d71db - -build: - number: 0 - noarch: generic - rpaths: - - lib/R/lib/ - - lib/ - -requirements: - host: - - r-base - - bioconductor-rdisop - - r-envipat - - r-plyr - run: - - r-base - - bioconductor-rdisop - - r-envipat - - r-plyr - -test: - commands: - - $R -e "library('InterpretMSSpectrum')" - -about: - home: http://dx.doi.org/10.1021/acs.analchem.6b02743 - license: GPL-3.0-only - summary: Annotate and interpret deconvoluted mass spectra (mass*intensity pairs) from high - resolution mass spectrometry devices. - license_family: GPL3 - license_file: - - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' From 6bbf5563108f217af8e3b430aed138ca1e908296 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 8 Jul 2023 14:01:09 -0600 Subject: [PATCH 065/101] Update zol to 1.3.3 (#41900) * Update zol to 1.3.3 * Update meta.yaml --------- Co-authored-by: Rauf Salamzade --- recipes/zol/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index 08b6d2b83410c..279428002b992 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.2" %} +{% set version = "1.3.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: a97b6ccd94909a11aacc4b6d2474dc02dabcf93da0693f239138c5c52f781518 + sha256: 384d10b488fe23a8100d05f6489d7c50fb8e8ae683f4ae634e1a2394a1194282 build: number: 0 @@ -51,6 +51,7 @@ requirements: - slclust - trimal - gzip + - miniprot =0.7 test: commands: From cea6ee396722799ea80e133d3de2540ce9dfebbd Mon Sep 17 00:00:00 2001 From: Yekai Zhou Date: Sun, 9 Jul 2023 19:57:57 +0800 Subject: [PATCH 066/101] update clair3 (#41902) * update clair3 * update clair3 --- recipes/duet/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/duet/meta.yaml b/recipes/duet/meta.yaml index 754abcd45de0c..be46b8f81a43c 100644 --- a/recipes/duet/meta.yaml +++ b/recipes/duet/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6" %} +{% set version = "1.0" %} package: name: duet @@ -6,7 +6,7 @@ package: source: url: https://github.com/yekaizhou/duet/archive/v{{ version }}.tar.gz - sha256: 09fd6ab5da6184067d682ab9a78f2bea1fea21c60b7f4f88454a60637bebd34e + sha256: 0b02ab9b2ff25b15ad6703ca99e6d11a3ffaf6981f28a9129ca6be0385e62553 requirements: host: @@ -14,7 +14,7 @@ requirements: - pip run: - python =3.9.0 - - clair3 =0.1.12 + - clair3 =1.0.3 - sniffles =2.0.7 - cutesv =2.0.2 - svim =1.4.2 From 482910691c245ddd157e033ee76bbacb0b319b3a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 9 Jul 2023 15:08:20 -0600 Subject: [PATCH 067/101] Update zol to 1.3.5 (#41907) * Update zol to 1.3.4 * Update zol to 1.3.5 --- recipes/zol/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index 279428002b992..ce236ced5dac2 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.3" %} +{% set version = "1.3.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: 384d10b488fe23a8100d05f6489d7c50fb8e8ae683f4ae634e1a2394a1194282 + sha256: 7581c2aad14c7fb6d11f89d3823c8850d23da267016945c552b701a6d1b5273b build: number: 0 From a057075f2b9bb09f53931ac66bbc940cd0472515 Mon Sep 17 00:00:00 2001 From: Leonid Kostrykin Date: Mon, 10 Jul 2023 00:28:15 +0200 Subject: [PATCH 068/101] adds dependency `scikit-image <=0.19` for superdsm (#41908) --- recipes/superdsm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/superdsm/meta.yaml b/recipes/superdsm/meta.yaml index 74b82f0dfcf60..12aa1e1c73a4d 100644 --- a/recipes/superdsm/meta.yaml +++ b/recipes/superdsm/meta.yaml @@ -12,7 +12,7 @@ source: sha256: f55abbd6818a66886ddfe3f7fd9c5dd93c63ed2b6e3179552106e560a000ad5f build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv " @@ -27,7 +27,7 @@ requirements: - ipython >=7.31.1 - numpy >=1.18,<2.0 - scipy >=1.6.3,<2.0 - - scikit-image >=0.18,<1.0 + - scikit-image >=0.18,<=0.19 - dill >=0.3.2 - cvxopt >=1.2.6,<2.0 - cvxpy >=1.1.13,<2.0 From 520de0cca6defc818ddcc673138ef3e3076f3a5d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 9 Jul 2023 22:16:16 -0600 Subject: [PATCH 069/101] Update simpleaf to 0.14.1 (#41913) --- recipes/simpleaf/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/simpleaf/meta.yaml b/recipes/simpleaf/meta.yaml index 875edc17f3537..c9348e6543f68 100644 --- a/recipes/simpleaf/meta.yaml +++ b/recipes/simpleaf/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.14.0" %} +{% set version = "0.14.1" %} package: name: simpleaf @@ -10,7 +10,7 @@ build: source: url: https://github.com/COMBINE-lab/simpleaf/archive/v{{ version }}.tar.gz - sha256: 316e915b4693765202da5deb8937ee826b3b19ed8c8f6bc5508329e3edf4a0b0 + sha256: 82b8c6210ffc668bd97abefa316705416ae0e511fba2fdd103fafc74a0e32f16 requirements: build: From ac6d96eca0fbee0aef74aecb7726618ca9d93c01 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Mon, 10 Jul 2023 03:09:51 -0500 Subject: [PATCH 070/101] Update tobias to 0.15.1 (#41912) --- build-fail-blacklist | 1 - recipes/tobias/build.sh | 3 --- recipes/tobias/meta.yaml | 55 ++++++++++++++++++++++++---------------- 3 files changed, 33 insertions(+), 26 deletions(-) delete mode 100644 recipes/tobias/build.sh diff --git a/build-fail-blacklist b/build-fail-blacklist index 352da75279a7b..93843e2f4fef0 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -6,7 +6,6 @@ recipes/octopus recipes/bttcmp recipes/bttoxin_scanner recipes/cgat-apps -recipes/tobias recipes/hatchet recipes/hail recipes/monocle3-cli diff --git a/recipes/tobias/build.sh b/recipes/tobias/build.sh deleted file mode 100644 index e45c73d5420b0..0000000000000 --- a/recipes/tobias/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/usr/bin/env bash - -$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/tobias/meta.yaml b/recipes/tobias/meta.yaml index bc14b28581a54..8442fbfc99e50 100644 --- a/recipes/tobias/meta.yaml +++ b/recipes/tobias/meta.yaml @@ -1,63 +1,74 @@ -{% set version = "0.13.3" %} +{% set name = "TOBIAS" %} +{% set version = "0.15.1" %} +{% set sha256 = "751416e72ea9fd0c7b857a586dc32be981370abdd8b8e6a925671041ced3b104" %} package: - name: tobias + name: {{ name|lower }} version: {{ version }} source: - url: https://pypi.io/packages/source/t/tobias/tobias-{{ version }}.tar.gz - sha256: 96f95b38f4353179cf1f5c79fdb07ec51f55a2cd3497bb63d6bb78f038c845e2 + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/tobias-{{ version }}.tar.gz + sha256: {{ sha256 }} build: - number: 1 - # Skipping py>=38 because dependency moods does not have Py3.8 builds. - skip: True # [py<30 or py>=38] + number: 0 + skip: True # [py < 37] + script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps -vv + entry_points: + - TOBIAS=tobias.TOBIAS:main requirements: build: - {{ compiler('c') }} host: - python - - setuptools - cython + - pip - numpy run: - python - - {{ pin_compatible('numpy') }} - scipy - pysam + - pybedtools - matplotlib-base >=2 - scikit-learn - pandas - pypdf2 - xlsxwriter - - pyBigWig - - moods - - pybedtools - adjusttext + - pybigwig >=0.3 + - moods - svist4get >=1.2.24 - - xgboost >=0.71 - - boto3 - - pyyaml >=5.1 - - seaborn >=0.9.1 - logomaker + - seaborn >=0.9.1 + - boto3 + - pyyaml >5.1 - kneed - - importlib_metadata + - xgboost >=0.71 + - importlib-metadata + - {{ pin_compatible('numpy') }} test: + imports: + - tobias commands: - - "TOBIAS --help" + - TOBIAS --help about: - home: https://github.com/loosolab/TOBIAS/ - doc_url: https://github.com/loosolab/TOBIAS/wiki + home: 'https://github.com/loosolab/TOBIAS' + summary: 'Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal' license: MIT - summary: Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal + license_file: LICENSE + doc_url: 'https://github.com/loosolab/TOBIAS/wiki' + dev_url: 'https://pypi.org/project/tobias/' description: | TOBIAS (Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal) is a collection - of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data. + of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data. extra: recipe-maintainers: - msbentsen - jenzopr + identifiers: + - biotools:TOBIAS + - doi:10.1038/s41467-020-18035-1 From 4e1a0d21c3919425c21cbb40cab706e9d13a3921 Mon Sep 17 00:00:00 2001 From: Jaebeom Kim <68528165+jaebeom-kim@users.noreply.github.com> Date: Mon, 10 Jul 2023 17:58:29 +0900 Subject: [PATCH 071/101] Metabuli 1.0.1 (#41914) Update Metabuli package to version v1.0.1 --- recipes/metabuli/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/metabuli/meta.yaml b/recipes/metabuli/meta.yaml index bdd2fb87fd432..20d813fdcfed8 100644 --- a/recipes/metabuli/meta.yaml +++ b/recipes/metabuli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.0.0" %} -{% set sha256 = "07d60f0044aafcb2361c5a571cb7bf56b981feba3b0195ba139c863fc2340938" %} +{% set version = "1.0.1" %} +{% set sha256 = "544926b73e7e0ed7c34d5f4f76e78e483261e5b13db6a6bb45217551bce1fae0" %} package: name: metabuli From 719653bfd243b277b003818400faf0e296dc5f18 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 10 Jul 2023 04:20:59 -0600 Subject: [PATCH 072/101] Update gffutils to 0.12 (#41836) Co-authored-by: Christian Brueffer --- recipes/gffutils/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gffutils/meta.yaml b/recipes/gffutils/meta.yaml index 56d4ceea83e37..f1f35d06d9903 100644 --- a/recipes/gffutils/meta.yaml +++ b/recipes/gffutils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gffutils" %} -{% set version = "0.11.1" %} -{% set sha256 = "ca7bf814d600b389bb2d5c403dd279755118cb1476c19c6f7aecb8c51a84263c" %} +{% set version = "0.12" %} +{% set sha256 = "b31e261db5bd8737cb712c361c129eb2c373ef62f03b62770320589f10da1983" %} package: name: "{{ name|lower }}" From 7cd1bac5286704cf356c269780945117521c8f0b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 10 Jul 2023 04:27:59 -0600 Subject: [PATCH 073/101] Update annonars to 0.12.9 (#41915) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 18984e86e4d4a..759db79c01021 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.12.8" %} +{% set version = "0.12.9" %} package: name: annonars @@ -10,7 +10,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5a1087440f0b136b2c1a4d5fb884fd2af15744831bf77636e3767ba416ed1df8 + sha256: 6e1869f4965bd096b60c386253f6a85879094ad50b01541c6df04f8225f87cdc requirements: build: From c82b72699aa41d78a49bfec697e00a5032820527 Mon Sep 17 00:00:00 2001 From: Tom Schoonjans Date: Mon, 10 Jul 2023 16:13:21 +0100 Subject: [PATCH 074/101] Update arvados-python-client: fix dependencies and install with pip (#41854) * Update dependencies and install with pip * Add minimum version constraint on setuptools in host section --- recipes/arvados-python-client/build.sh | 5 ++--- recipes/arvados-python-client/meta.yaml | 26 +++++++++++-------------- 2 files changed, 13 insertions(+), 18 deletions(-) diff --git a/recipes/arvados-python-client/build.sh b/recipes/arvados-python-client/build.sh index e7ecc9da161d1..29528342ab7a9 100755 --- a/recipes/arvados-python-client/build.sh +++ b/recipes/arvados-python-client/build.sh @@ -1,4 +1,3 @@ #!/bin/bash -sed -i.bak 's/pyasn1-modules==0.0.5/pyasn1-modules>=0.0.5/' setup.py -sed -i.bak 's/google-api-python-client==/google-api-python-client>=/' setup.py -$PYTHON setup.py install --single-version-externally-managed --record=record.txt +$PYTHON -m pip install . --no-deps -vv + diff --git a/recipes/arvados-python-client/meta.yaml b/recipes/arvados-python-client/meta.yaml index 5198cf9fcb323..a1636583d9bc6 100644 --- a/recipes/arvados-python-client/meta.yaml +++ b/recipes/arvados-python-client/meta.yaml @@ -10,33 +10,29 @@ source: build: noarch: python - number: 0 + number: 1 requirements: host: - python >=3 - - setuptools - - ciso8601 >=2.0.0 - - future - - google-api-python-client <1.7,>=1.6.2 - - google-auth <2 - - httplib2 - - pycurl >=7.19.5.1,<7.45.0 - - ruamel.yaml >=0.15.54 - - ws4py >=0.4.2 - - protobuf <4.0.0 + - setuptools >=40.3.0 + - pip run: - python >=3 - - setuptools + - setuptools >=40.3.0 - ciso8601 >=2.0.0 - future - - google-api-python-client <1.7,>=1.6.2 + - google-api-core <2.11.0 # 2.11.0rc1 is incompatible with google-auth<2 + - google-api-python-client >=2.1.0 - google-auth <2 - - httplib2 + - httplib2 >=0.9.2,<0.20.2 - pycurl >=7.19.5.1,<7.45.0 - - ruamel.yaml >=0.15.54 + - ruamel.yaml >=0.15.54,<0.17.22 + - typing-extensions >=3.7.4 - ws4py >=0.4.2 - protobuf <4.0.0 + - pyparsing <3 + - dataclasses test: imports: From acd0dfe5e9058e65e70778a1249e4d91fe402fd6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 10 Jul 2023 12:59:22 -0600 Subject: [PATCH 075/101] Update zol to 1.3.6 (#41926) --- recipes/zol/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index ce236ced5dac2..670bc4bd49e89 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.5" %} +{% set version = "1.3.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: 7581c2aad14c7fb6d11f89d3823c8850d23da267016945c552b701a6d1b5273b + sha256: 7a7dc68fd2b119a49e19a825fedd889fd167693b514fc29fcc4e0be3c7fa6706 build: number: 0 From 704f310cd315f7a3fcfda88f0cd0eeb2c97533fe Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Mon, 10 Jul 2023 23:20:30 +0200 Subject: [PATCH 076/101] Add VirAmp-Hub (#41925) --- recipes/viramp-hub/meta.yaml | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 recipes/viramp-hub/meta.yaml diff --git a/recipes/viramp-hub/meta.yaml b/recipes/viramp-hub/meta.yaml new file mode 100644 index 0000000000000..9849681674b42 --- /dev/null +++ b/recipes/viramp-hub/meta.yaml @@ -0,0 +1,36 @@ +{% set package_name = "viramp-hub" %} +{% set name = "viramp_hub" %} +{% set version = "0.1.0" %} +{% set sha256 = "a930e2caed01d94a96decae239e6dcc0f8c83cc9eaef393c53641a3d61269ffc" %} + +package: + name: "{{ package_name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: "{{ sha256 }}" + +build: + script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed --no-cache-dir -vvv ." + noarch: python + number: 0 + +requirements: + host: + - python >=3.6 + - pip + run: + - python >=3.6 + +test: + commands: + - scheme-convert -h + +about: + home: "https://github.com/wm75/viramp-hub" + license: MIT + license_family: MIT + license_file: LICENSE + summary: "VirAmp-Hub lets you manipulate/convert viral amplicon/primer scheme information." + doc_url: "https://github.com/wm75/viramp-hub" From 485482b28d1b7cfb8b9cec3c5b2fd4fcd0aa3f46 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 10 Jul 2023 22:16:18 -0600 Subject: [PATCH 077/101] Update r-recetox-aplcms to 0.12.0 (#41916) --- recipes/r-recetox-aplcms/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-recetox-aplcms/meta.yaml b/recipes/r-recetox-aplcms/meta.yaml index 8f86685424f2a..a8506f6814e97 100644 --- a/recipes/r-recetox-aplcms/meta.yaml +++ b/recipes/r-recetox-aplcms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "recetox-aplcms" %} -{% set version = "0.11.0" %} +{% set version = "0.12.0" %} {% set github = "https://github.com/RECETOX" %} package: @@ -8,7 +8,7 @@ package: source: url: "{{ github }}/recetox-aplcms/archive/refs/tags/v{{ version }}.tar.gz" - sha256: e956f401bf75b5733111fd0316b2abe76ae93d6735a49aa58b864aad321555e6 + sha256: c76715e50a442b45f46f79120af6f382965f9a8de63bf0f624eb132478b6ed2c build: number: 0 From 03e4a667913e3aa4327214ffcb9c91a0ca8b4ecc Mon Sep 17 00:00:00 2001 From: Romain Derelle Date: Tue, 11 Jul 2023 11:49:30 +0100 Subject: [PATCH 078/101] add fastlin to Bioconda channel (#41937) Co-authored-by: Romain Derelle --- recipes/fastlin/meta.yaml | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 recipes/fastlin/meta.yaml diff --git a/recipes/fastlin/meta.yaml b/recipes/fastlin/meta.yaml new file mode 100644 index 0000000000000..b47aea5fb982f --- /dev/null +++ b/recipes/fastlin/meta.yaml @@ -0,0 +1,28 @@ +{% set name = "fastlin" %} +{% set version = "0.1.0" %} + +package: + name: {{ name|lower}} + version: {{ version }} + +source: + url: https://github.com/rderelle/fastlin/archive/v{{ version }}.tar.gz + sha256: 80c1dd7ce797836c6b132c303321035866a9bb234484603ea6e5e6dee38b0d00 + +build: + number: 0 + script: "cargo install --no-track --locked --verbose --root \"${PREFIX}\" --path ." + +requirements: + build: + - {{ compiler('rust') }} + +test: + commands: + - fastlin -h + +about: + home: https://github.com/rderelle/fastlin + license: MIT + license_file: LICENSE + summary: fastlin, ultra-fast MTBC lineage typing \ No newline at end of file From e91e28d3c246472ef2bc7e54f2aa46eeed563424 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Adri=C3=A1n=20Diaz?= Date: Tue, 11 Jul 2023 13:49:48 +0200 Subject: [PATCH 079/101] Update b2btools to 3.0.6 (#41841) * Update b2btools to 3.0.6 * Update meta using the skeleton coming from PyPi package * Fix linting issues * Update meta.yaml in order to include bioconda dependencies * Update meta.yaml * Update meta.yaml * Update run_test.sh --- recipes/b2btools/meta.yaml | 109 ++++++++--- recipes/b2btools/run_test.sh | 339 +++++++++++++++++++++++++++++++++-- 2 files changed, 414 insertions(+), 34 deletions(-) diff --git a/recipes/b2btools/meta.yaml b/recipes/b2btools/meta.yaml index f19ea2e1648a2..ee132b4d4c57d 100644 --- a/recipes/b2btools/meta.yaml +++ b/recipes/b2btools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "b2bTools" %} -{% set version = "3.0.5" %} +{% set version = "3.0.6" %} package: name: "{{ name|lower }}" @@ -7,43 +7,104 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 9c3a1e539d1bdbfeecc29e878bb98f05590227d90f838846fb01152a49c509b4 + sha256: 3617afcfe76cbff3a6bfad4060f962568565fb691b978f87d8db78cde97da58b build: number: 0 script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" noarch: python + entry_points: + - b2bTools = b2bTools.__main__:main requirements: host: - - python >3.6,<3.10 + - python >=3.7,<3.10 - pip run: - - biopython - - joblib - - matplotlib-base - - networkx - - numpy - - pandas - - pillow - - pomegranate - - python >3.6,<3.10 - - pyyaml - - requests - - scikit-learn >=1.0.1 - - scipy - - six - - threadpoolctl - - pytorch >=1.8.0 - - torchvision + - biopython ==1.81 + - certifi ==2023.5.7 + - charset-normalizer ==3.1.0 + - cycler ==0.11.0 + - exceptiongroup ==1.1.1 + - fonttools ==4.38.0 + - hmmer + - idna ==3.4 + - importlib-metadata ==6.7.0 + - iniconfig ==2.0.0 + - joblib ==1.2.0 + - kiwisolver ==1.4.4 + - matplotlib-base ==3.5.3 + - networkx ==2.6.3 + - numpy ==1.21.6 #[py37] + - numpy ==1.24.4 #[py38, py39] + - packaging ==23.1 + - pandas >=1.1,<=1.2 + - pillow ==9.5.0 + - pluggy ==1.2.0 + - pomegranate ==0.14.8 + - pyparsing ==3.1.0 + - python-dateutil ==2.8.2 + - pytorch >=1.8.0 #,<1.13.1 + - pytz ==2023.3 + - PyYAML ==6.0 + - requests ==2.31.0 + - scikit-learn ==1.0.1 + - scipy ==1.10.1 + - t-coffee + - threadpoolctl ==3.1.0 + - tomli ==2.0.1 + - tqdm ==4.65.0 + - typing_extensions ==4.6.3 + - urllib3 ==1.26.6 + - zipp ==3.15.0 + test: imports: - b2bTools - b2bTools.general + - b2bTools.general.bmrb + - b2bTools.general.ccpn + - b2bTools.general.ccpn.format + - b2bTools.general.ccpn.format.general + - b2bTools.general.ccpn.format.nmrStar + - b2bTools.general.ccpn.general + - b2bTools.general.ccpn.universal - b2bTools.general.parsers - b2bTools.multipleSeq + - b2bTools.nmr + - b2bTools.nmr.shiftCrypt + - b2bTools.nmr.shiftCrypt.models + - b2bTools.nmr.shiftCrypt.shiftcrypt_pkg - b2bTools.singleSeq + - b2bTools.singleSeq.Agmata + - b2bTools.singleSeq.Agmata.bin + - b2bTools.singleSeq.Agmata.marshalled + - b2bTools.singleSeq.Agmata.sources + - b2bTools.singleSeq.DisoMine + - b2bTools.singleSeq.DisoMine.vector_builder + - b2bTools.singleSeq.DisoMine.vector_builder.psipred + - b2bTools.singleSeq.DisoMine.vector_builder.psipred.bin + - b2bTools.singleSeq.DisoMine.vector_builder.psipred.bin.linux + - b2bTools.singleSeq.DisoMine.vector_builder.psipred.bin.osx + - b2bTools.singleSeq.DisoMine.vector_builder.psipred.data + - b2bTools.singleSeq.DynaMine + - b2bTools.singleSeq.DynaMine.models + - b2bTools.singleSeq.DynaMine.models.backbone + - b2bTools.singleSeq.DynaMine.models.coil + - b2bTools.singleSeq.DynaMine.models.helix + - b2bTools.singleSeq.DynaMine.models.ppII + - b2bTools.singleSeq.DynaMine.models.sheet + - b2bTools.singleSeq.DynaMine.models.sidechain + - b2bTools.singleSeq.EFoldMine + - b2bTools.singleSeq.EFoldMine.models + - b2bTools.singleSeq.PSPer + - b2bTools.singleSeq.PSPer.hmmer_research + - b2bTools.singleSeq.PSPer.marshalled + - b2bTools.singleSeq.PSPer.source - b2bTools.wrapper_source + commands: + - b2bTools --help + - b2bTools --version about: home: "https://bio2byte.be/" @@ -53,17 +114,21 @@ about: summary: "bio2Byte software suite to predict protein biophysical properties from their amino-acid sequences" description: | This package provides you with structural predictions for protein sequences made by the Bio2Byte group which researches the relation between protein sequence and biophysical behavior. - List of available predictors: + List of available predictors: - Dynamine: Fast predictor of protein backbone dynamics using only sequence information as input. The version here also predicts side-chain dynamics and secondary structure predictors using the same principle. - Disomine: Predicts protein disorder with recurrent neural networks not directly from the amino acid sequence, but instead from more generic predictions of key biophysical properties, here protein dynamics, secondary structure, and early folding. - EfoldMine: Predicts from the primary amino acid sequence of a protein, which amino acids are likely involved in early folding events. - AgMata: Single-sequence-based predictor of protein regions that are likely to cause beta-aggregation. + - PSPer: PSP (Phase Separating Protein) predicts whether a protein is likely to phase-separate with a particular mechanism involving RNA interacts (FUS-like proteins). doc_url: https://bio2byte.be/b2btools/package-documentation dev_url: https://pypi.org/project/b2bTools/ extra: - author: + author: - Wim Vranken + recipe-maintainers: + - Adrián Díaz (@agdiaz) + - Jose Gavaldá-García (@GavaldaGarcia) maintainers: - Adrián Díaz (@agdiaz) - Jose Gavaldá-García (@GavaldaGarcia) diff --git a/recipes/b2btools/run_test.sh b/recipes/b2btools/run_test.sh index a6f65cb6c66e5..040ee3b063011 100755 --- a/recipes/b2btools/run_test.sh +++ b/recipes/b2btools/run_test.sh @@ -1,25 +1,340 @@ #!/bin/bash -echo Testing b2bTools +# Test locally? Read these articles: +# - https://bioconda.github.io/contributor/building-locally.html +# - https://docs.openfree.energy/en/stable/installation.html -cat <> input_example.fasta +cat <> ./input_example.fasta >SEQ_1 MEDLNVVDSINGAGSWLVANQALLLSYAVNIVAALAIIIVGLIIARMISNAVNRLMISRK -IDATVADFLSALVRYGIIAFTLIAALGRVGVQTASVIAVLGAAGLAVGLALQGSLSNLAA -GVLLVMFRPFRAGEYVDLGGVAGTVLSVQIFSTTMRTADGKIIVIPNGKIIAGNIINFSR + +>SEQ_2 EPVRRNEFIIGVAYDSDIDQVKQILTNIIQSEDRILKDREMTVRLNELGASSINFVVRVW -SNSGDLQNVYWDVLERIKREFDAAGISFPYPQMDVNFKRVKEDKAA EOT -python -m b2bTools --help +cat <> ./small_alignment.clustal +CLUSTAL O(1.2.4) multiple sequence alignment + + +SEQ_1 -VYVGNLGNNG 10 +SEQ_2 RVRCGCLTRG- 10 + * * * .. +EOT + +print_message() { + current_time=$(date +"%T") + echo "[$current_time - b2bTools] run_test.sh: $1" +} + +preconditions() { + print_message "Testing HMMER dependencies" + + hmmalign -h + hmmsearch -h + + print_message "Testing T-Coffee dependencies" + t_coffee --help + + print_message "Testing b2bTools itself" + b2bTools -h +} + +postconditions() { + print_message "Removing testing files" + + rm ./input_example.fasta ./small_alignment.clustal +} + +scenario_single_seq_without_agmata_psper() { + print_message "1.1) Testing b2bTools for Single Seq mode without AgMata nor PSPer" + + # Check if the status code is non-zero and exit with an error code + if [ $status -ne 0 ]; then + echo "Error: b2bTools command failed with status code $status" + exit $status + fi + + python -m b2bTools \ + --dynamine \ + --disomine \ + --efoldmine \ + --input_file ./input_example.fasta \ + --output_json_file ./input_example.fasta.json \ + --output_tabular_file ./input_example.fasta.csv \ + --metadata_file ./input_example.fasta.meta.csv + status=$? + + # Check if the status code is non-zero and exit with an error code + if [ $status -ne 0 ]; then + print_message "1.1) Error: b2bTools command failed with status code $status" + exit $status + fi + + # Validate the presence and content of output files + files=("input_example.fasta.json" "input_example.fasta.csv" "input_example.fasta.meta.csv") + for file in "${files[@]}"; do + if [ ! -f "$file" ]; then + print_message "1.1) Error: Output file $file not found" + exit 1 + fi + + # Check if the file is a CSV and has more than one row + if [[ "$file" == *.csv ]]; then + row_count=$(wc -l < "$file") + if [ $row_count -le 1 ]; then + print_message "1.1) Error: Output file $file is a CSV with less than two rows" + exit 1 + fi + fi + + # Cleanup: remove input and output files + if [ -f "$file" ]; then + rm "$file" + fi + done + + print_message "1.1) Testing b2bTools for Single Seq mode finished with success" +} + +scenario_single_seq_only_psper() { + print_message "1.2) Testing b2bTools for Single Seq mode using PSPer" + + python -m b2bTools \ + --psper \ + --input_file ./input_example.fasta \ + --output_json_file ./input_example.fasta.json \ + --output_tabular_file ./input_example.fasta.csv \ + --metadata_file ./input_example.fasta.meta.csv + status=$? + + # Check if the status code is non-zero and exit with an error code + if [ $status -ne 0 ]; then + print_message "1.2) Error: b2bTools command failed with status code $status" + exit $status + fi + + # Validate the presence and content of output files + files=("input_example.fasta.json" "input_example.fasta.csv" "input_example.fasta.meta.csv") + for file in "${files[@]}"; do + if [ ! -f "$file" ]; then + print_message "1.2)Error: Output file $file not found" + exit 1 + fi + + # Check if the file is a CSV and has more than one row + if [[ "$file" == *.csv ]]; then + row_count=$(wc -l < "$file") + if [ $row_count -le 1 ]; then + print_message "1.2) Error: Output file $file is a CSV with less than two rows" + exit 1 + fi + fi + + # Cleanup: remove input and output files + if [ -f "$file" ]; then + rm "$file" + fi + done + + print_message "1.2) Testing b2bTools for Single Seq mode finished with success" +} + +scenario_single_seq_only_agmata() { + print_message "1.3) Testing b2bTools for Single Seq mode using Agmata" + + python -m b2bTools \ + --agmata \ + --input_file ./input_example.fasta \ + --output_json_file ./input_example.fasta.json \ + --output_tabular_file ./input_example.fasta.csv \ + --metadata_file ./input_example.fasta.meta.csv + status=$? + + # Check if the status code is non-zero and exit with an error code + if [ $status -ne 0 ]; then + print_message "1.3) Error: b2bTools command failed with status code $status" + exit $status + fi + + # Validate the presence and content of output files + files=("input_example.fasta.json" "input_example.fasta.csv" "input_example.fasta.meta.csv") + for file in "${files[@]}"; do + if [ ! -f "$file" ]; then + print_message "1.3)Error: Output file $file not found" + exit 1 + fi + + # Check if the file is a CSV and has more than one row + if [[ "$file" == *.csv ]]; then + row_count=$(wc -l < "$file") + if [ $row_count -le 1 ]; then + print_message "1.3) Error: Output file $file is a CSV with less than two rows" + exit 1 + fi + fi + + # Cleanup: remove input and output files + if [ -f "$file" ]; then + rm "$file" + fi + done + + print_message "1.3) Testing b2bTools for Single Seq mode finished with success" +} + +scenario_msa_without_agmata_psper() { + print_message "2.1) Testing b2bTools for MSA mode without AgMata nor PSPer" + + python -m b2bTools \ + --mode msa \ + --dynamine \ + --disomine \ + --efoldmine \ + --input_file ./small_alignment.clustal \ + --output_json_file ./small_alignment.clustal.json \ + --output_tabular_file ./small_alignment.clustal.csv \ + --metadata_file ./small_alignment.clustal.meta.csv \ + --distribution_json_file ./small_alignment.clustal.distrib.json \ + --distribution_tabular_file ./small_alignment.clustal.distrib.csv + + status=$? + + # Check if the status code is non-zero and exit with an error code + if [ $status -ne 0 ]; then + print_message "2.1) Error: b2bTools command failed with status code $status" + exit $status + fi + + # Validate the presence and content of output files + files=("small_alignment.clustal.json" "small_alignment.clustal.csv" "small_alignment.clustal.meta.csv" "small_alignment.clustal.distrib.json" "small_alignment.clustal.distrib.csv") + for file in "${files[@]}"; do + if [ ! -f "$file" ]; then + print_message "2.1) Error: Output file $file not found" + exit 1 + fi + + # Check if the file is a CSV and has more than one row + if [[ "$file" == *.csv ]]; then + row_count=$(wc -l < "$file") + if [ $row_count -le 1 ]; then + print_message "2.1) Error: Output file $file is a CSV with less than two rows" + exit 1 + fi + fi + + # Cleanup: remove input and output files + if [ -f "$file" ]; then + rm "$file" + fi + done + + print_message "2.1) Testing b2bTools for MSA mode finished with success" +} + +scenario_msa_only_psper() { + print_message "2.2) Testing b2bTools for MSA mode with PSPer" + + python -m b2bTools \ + --mode msa \ + --psper \ + --input_file ./small_alignment.clustal \ + --output_json_file ./small_alignment.clustal.json \ + --output_tabular_file ./small_alignment.clustal.csv \ + --metadata_file ./small_alignment.clustal.meta.csv \ + --distribution_json_file ./small_alignment.clustal.distrib.json \ + --distribution_tabular_file ./small_alignment.clustal.distrib.csv + + status=$? + + # Check if the status code is non-zero and exit with an error code + if [ $status -ne 0 ]; then + print_message "2.1) Error: b2bTools command failed with status code $status" + exit $status + fi + + # Validate the presence and content of output files + files=("small_alignment.clustal.json" "small_alignment.clustal.csv" "small_alignment.clustal.meta.csv" "small_alignment.clustal.distrib.json" "small_alignment.clustal.distrib.csv") + for file in "${files[@]}"; do + if [ ! -f "$file" ]; then + print_message "2.1) Error: Output file $file not found" + exit 1 + fi + + # Check if the file is a CSV and has more than one row + if [[ "$file" == *.csv ]]; then + row_count=$(wc -l < "$file") + if [ $row_count -le 1 ]; then + print_message "2.1) Error: Output file $file is a CSV with less than two rows" + exit 1 + fi + fi + + # Cleanup: remove input and output files + if [ -f "$file" ]; then + rm "$file" + fi + done +} + +scenario_msa_only_agmata() { + print_message "2.2) Testing b2bTools for MSA mode with PSPer" + + python -m b2bTools \ + --mode msa \ + --agmata \ + --input_file ./small_alignment.clustal \ + --output_json_file ./small_alignment.clustal.json \ + --output_tabular_file ./small_alignment.clustal.csv \ + --metadata_file ./small_alignment.clustal.meta.csv \ + --distribution_json_file ./small_alignment.clustal.distrib.json \ + --distribution_tabular_file ./small_alignment.clustal.distrib.csv + + status=$? + + # Check if the status code is non-zero and exit with an error code + if [ $status -ne 0 ]; then + print_message "2.1) Error: b2bTools command failed with status code $status" + exit $status + fi + + # Validate the presence and content of output files + files=("small_alignment.clustal.json" "small_alignment.clustal.csv" "small_alignment.clustal.meta.csv" "small_alignment.clustal.distrib.json" "small_alignment.clustal.distrib.csv") + for file in "${files[@]}"; do + if [ ! -f "$file" ]; then + print_message "2.1) Error: Output file $file not found" + exit 1 + fi + + # Check if the file is a CSV and has more than one row + if [[ "$file" == *.csv ]]; then + row_count=$(wc -l < "$file") + if [ $row_count -le 1 ]; then + print_message "2.1) Error: Output file $file is a CSV with less than two rows" + exit 1 + fi + fi + + # Cleanup: remove input and output files + if [ -f "$file" ]; then + rm "$file" + fi + done +} + +print_message "Running test scenarios" -python -m b2bTools -file ./input_example.fasta -identifier TEST -output ./results_b2b.json -dynamine -disomine -efoldmine -agmata +preconditions -rm ./input_example.fasta +# Scenarios for Single Sequence input +scenario_single_seq_without_agmata_psper +scenario_single_seq_only_psper +scenario_single_seq_only_agmata -cat ./results_b2b.json +# Scenarios for Multiple Sequence Alignment input +scenario_msa_without_agmata_psper +scenario_msa_only_psper +scenario_msa_only_agmata -rm ./results_b2b.json +postconditions -echo "" -echo Test finished \ No newline at end of file +print_message "All test scenarios have been executed with success" From 1a578fb6d7386d2de4f60892a40ee43033a15c41 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 11 Jul 2023 05:50:40 -0600 Subject: [PATCH 080/101] Update ska2 to 0.3.1 (#41917) Co-authored-by: John Lees --- recipes/ska2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/ska2/meta.yaml b/recipes/ska2/meta.yaml index 2df93be40d85f..067ac44d6ce3c 100644 --- a/recipes/ska2/meta.yaml +++ b/recipes/ska2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ska2" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: {{ name|lower}} @@ -7,7 +7,7 @@ package: source: url: https://github.com/bacpop/ska.rust/archive/v{{ version }}.tar.gz - sha256: 21ce3547fc3f6f035739381dc39a3621afafc96991659187d175bed630ef75c3 + sha256: f4657574974b7bd0ec0a7fc3a9a752a16b433d3865c16e85f64c372b7cd78ad6 build: number: 0 From ade49f01edc33d5a76ec188aeee650b3bc345b07 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 11 Jul 2023 11:14:18 -0600 Subject: [PATCH 081/101] Update svjedi-graph to 1.2.0 (#41887) * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update svjedi-graph to 1.2.0 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/svjedi-graph/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/svjedi-graph/meta.yaml b/recipes/svjedi-graph/meta.yaml index 61b0ca8e3a4e8..1f53c0c85f13c 100644 --- a/recipes/svjedi-graph/meta.yaml +++ b/recipes/svjedi-graph/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.1" %} -{% set sha256 = "b6b18604891e2c4fea94e7ad85ff049120f8cb9f95daf1a5329223a851e17195" %} +{% set version = "1.2.0" %} +{% set sha256 = "ec01f0fc9bc0814f1d42caf3af57f50ead8bc4b89aabd007f595c31a200a078c" %} package: name: svjedi-graph @@ -10,7 +10,7 @@ build: number: 0 source: - url: https://github.com/SandraLouise/SVJedi-graph/archive/v{{ version }}.tar.gz + url: https://github.com/SandraLouise/SVJedi-graph/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} requirements: From cd557835a97609d8244a5ecc28fcfcf194f821e2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 11 Jul 2023 12:29:08 -0600 Subject: [PATCH 082/101] Update wgd to 2.0.20 (#41954) --- recipes/wgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wgd/meta.yaml b/recipes/wgd/meta.yaml index e25a86caa93ac..406a9d28353b2 100644 --- a/recipes/wgd/meta.yaml +++ b/recipes/wgd/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.19" %} +{% set version = "2.0.20" %} package: name: "wgd" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/w/wgd/wgd-{{ version }}.tar.gz - sha256: 9f0dff110c6a734665060f23bf1dbe10776089a3babdd6a8c6168e3a19bdb8ba + sha256: a4e90266b6efb737b47140f7ed04594ab26904d67b11333674616574e8aa56a7 build: number: 0 From e24214c6baa1a1b0bae3d1bcd6d02df2252dc46d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 11 Jul 2023 16:36:14 -0600 Subject: [PATCH 083/101] Update fibertools-rs to 0.2.4 (#41958) --- recipes/fibertools-rs/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fibertools-rs/meta.yaml b/recipes/fibertools-rs/meta.yaml index 0c8689ba43b11..66b79fdecd273 100644 --- a/recipes/fibertools-rs/meta.yaml +++ b/recipes/fibertools-rs/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.2.3" %} +{% set version = "0.2.4" %} {% set name = "fibertools-rs" %} {% set build_number = "0" %} @@ -25,7 +25,7 @@ build: source: url: https://github.com/fiberseq/fibertools-rs/archive/v{{ version }}.tar.gz - sha256: ffd30d47848f1d063438f88e713997f9f6ce15fa4a5cb648164c5b97a8f63000 + sha256: 99cd36758af0f3302dbf00c3fe098bee5f12adc2b3eebf31653100adc4e5e740 requirements: build: From 5d7d1fb95ff1d32170a889b8c9ab7c6fc7ea3a35 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 11 Jul 2023 23:29:09 -0600 Subject: [PATCH 084/101] Update mehari to 0.6.1 (#41951) --- recipes/mehari/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index 5ee9d6f0add62..64fb2b7207308 100644 --- a/recipes/mehari/meta.yaml +++ b/recipes/mehari/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.6.0" %} -{% set sha256 = "4d64a4e20cb0600550625968f732e1ee09d23be02af2469d46d3160e00966ce2" %} +{% set version = "0.6.1" %} +{% set sha256 = "024598372c02ca2958465313a114494fcd9633e9a62292999b39984cef014064" %} package: name: mehari From 481db174648452f3af8d183d9804fa28abf92808 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 12 Jul 2023 02:58:20 -0600 Subject: [PATCH 085/101] Update panfeed to 1.5.1 (#41949) Co-authored-by: Marco Galardini --- recipes/panfeed/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/panfeed/meta.yaml b/recipes/panfeed/meta.yaml index 6f05f9ee6e50a..6d1fef35edd4a 100644 --- a/recipes/panfeed/meta.yaml +++ b/recipes/panfeed/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.5.0" %} +{% set version = "1.5.1" %} {% set name = "panfeed" %} package: @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 07535e0da4b7e0db4919133d77563b2712890f10904c4042996ad668996d71c6 + sha256: b5371a549d315c8f12339e6eeeb72cb0449d84b6a119959b05f689c3847fb203 build: entry_points: From 48d26c6047dabd3fc0cf4eda9ce1f6caf71b9554 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 12 Jul 2023 04:53:49 -0600 Subject: [PATCH 086/101] Update r-epic to 1.1.7 (#41964) --- recipes/r-epic/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-epic/meta.yaml b/recipes/r-epic/meta.yaml index f25ae51364552..f5fb84b3b01eb 100755 --- a/recipes/r-epic/meta.yaml +++ b/recipes/r-epic/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.6" %} +{% set version = "1.1.7" %} package: name: r-epic @@ -7,7 +7,7 @@ package: source: url: - https://github.com/GfellerLab/EPIC/archive/v{{ version }}.tar.gz - sha256: 13235239c92cc7851871abcd0110268312847cd12928d41940cea51e59d5749f + sha256: 795150b042606a9ab6efbf3b50145c4ee6b626ede5f344b3dd83045238b1f625 build: number: 0 From 485c85d2334b845b6340b089c1b81c7f1caff711 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 12 Jul 2023 04:56:37 -0600 Subject: [PATCH 087/101] Update coolpuppy to 1.1.0 (#41955) --- recipes/coolpuppy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/coolpuppy/meta.yaml b/recipes/coolpuppy/meta.yaml index 0d1aa703ecf2a..20b1a07ac40b8 100644 --- a/recipes/coolpuppy/meta.yaml +++ b/recipes/coolpuppy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "coolpuppy" %} -{% set version = "1.0.0" %} +{% set version = "1.1.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/open2c/coolpuppy/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 96e4c7a57b6a7621f4d5247d9b96d14d53df84d00da703a59ea29f446cf04ce5 + sha256: 02667b5c5f52bc3b5f25d9732b4fa04ffb9b31331180f7e1c072110bb3462d10 build: number: 0 From b373c3d7844e43b285f212be23d8a5683efe11cf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 12 Jul 2023 14:23:35 -0600 Subject: [PATCH 088/101] Update baltic to 0.2.1 (#41965) * Update baltic to 0.2.0 * Update baltic to 0.2.1 --- recipes/baltic/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/baltic/meta.yaml b/recipes/baltic/meta.yaml index 7b945b8ba9dc1..4d81e64812c2b 100644 --- a/recipes/baltic/meta.yaml +++ b/recipes/baltic/meta.yaml @@ -1,5 +1,5 @@ {% set name = "baltic" %} -{% set version = "0.1.8" %} +{% set version = "0.2.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e1a392b376b42861c4d33d92bce412ab92dc9b266f33949e83a78794de88d223 + sha256: 7b942c0c6ff5b4ab8b6663191a9a874db6e2ff6b149f32b205011fbc6fc41602 build: number: 0 From b77eb5b164941f54b7307c63960314d80efbbfb8 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 12 Jul 2023 21:21:28 -0600 Subject: [PATCH 089/101] Update hostile to 0.0.3 (#41967) --- recipes/hostile/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hostile/meta.yaml b/recipes/hostile/meta.yaml index 27facc3ec38bb..4c894e0531464 100644 --- a/recipes/hostile/meta.yaml +++ b/recipes/hostile/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.0.2" %} +{% set version = "0.0.3" %} package: name: hostile @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/h/hostile/hostile-{{ version }}.tar.gz - sha256: 1e583b611deff299319852476d38102ac6fafb3f69fe46c2e7459c36e2d566aa + sha256: efaef22a482cc7fab0217804f0112ac7795079cbbfb433cb0a2d0f456f8e16ac build: noarch: python From 196d49886110d067742bb22383954968b740c1c1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 13 Jul 2023 10:02:30 +0200 Subject: [PATCH 090/101] fix: pin compatible versions of vcflib in freebayes recipe (#41959) * pin compatible versions of vcflib * bump build number * try to remove vcflib from run * bump build number * dbg * dbg --- recipes/freebayes/meta.yaml | 6 +++--- recipes/vcflib/meta.yaml | 5 ++++- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/recipes/freebayes/meta.yaml b/recipes/freebayes/meta.yaml index e3f3489e24e82..12b4e2c7deb0e 100644 --- a/recipes/freebayes/meta.yaml +++ b/recipes/freebayes/meta.yaml @@ -9,7 +9,8 @@ source: sha256: 6016c1e58fdf34a1f6f77b720dd8e12e13a127f7cbac9c747e47954561b437f5 build: - number: 4 + number: 5 + skip: true # [osx] requirements: build: @@ -23,11 +24,10 @@ requirements: - bzip2 - htslib - tabixpp + - vcflib run: - - htslib - parallel - samtools - - vcflib - tabixpp test: diff --git a/recipes/vcflib/meta.yaml b/recipes/vcflib/meta.yaml index 3b610b0ad43f1..4987517e68da0 100644 --- a/recipes/vcflib/meta.yaml +++ b/recipes/vcflib/meta.yaml @@ -21,8 +21,10 @@ source: folder: zig-macos-x86_64-0.10.1 # [osx] build: - number: 0 + number: 1 skip: True # [osx] + run_exports: + - {{ pin_subpackage('vcflib') }} requirements: build: @@ -49,6 +51,7 @@ requirements: - jsoncpp - wfa2-lib + test: commands: - "vcfwave -h" From e38a8e2a8e12ff04f2bda8c61cf138dcbccd39fa Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 13 Jul 2023 02:03:04 -0600 Subject: [PATCH 091/101] Update jbrowse2 to 2.6.2 (#41974) --- recipes/jbrowse2/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jbrowse2/meta.yaml b/recipes/jbrowse2/meta.yaml index bb8bee713b54d..d1c1a972be05e 100644 --- a/recipes/jbrowse2/meta.yaml +++ b/recipes/jbrowse2/meta.yaml @@ -1,12 +1,12 @@ # When updating, check the @jbrowse/cli version in build.sh too -{% set version = "2.6.1" %} +{% set version = "2.6.2" %} package: name: jbrowse2 version: {{ version }} source: - sha256: 6249d00764a4c13bf7cb3d40ade53bc0eea021f47f2366aead16a191203ec5ac + sha256: 3de6b69d390047e8bc62829983ea3d48cf3b47e7e1e289c9707ba173b561ec48 url: https://github.com/GMOD/jbrowse-components/releases/download/v{{ version }}/jbrowse-web-v{{ version }}.zip build: From f4599a754be1bcfc9a69eb8d3045b2ea3295ad60 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 13 Jul 2023 04:21:32 -0600 Subject: [PATCH 092/101] Update icount-mini to 3.0.1 (#41966) --- recipes/icount-mini/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/icount-mini/meta.yaml b/recipes/icount-mini/meta.yaml index 6c14dfa4193ed..e25f9f8c32e2a 100644 --- a/recipes/icount-mini/meta.yaml +++ b/recipes/icount-mini/meta.yaml @@ -1,5 +1,5 @@ {% set name = "iCount-Mini" %} -{% set version = "3.0.0" %} +{% set version = "3.0.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: a6c62b0b7dc0f0752ab693041edfab6dfec2510c5114e28ee8688dfc78a0a7f4 + sha256: 795e2ee77c5a23c96c01d4144c5b78103982ec3aa7274fea8f3ed94c0fd511ac build: number: 0 From 6871e8504c8726eae7ab2b009087f763bc198852 Mon Sep 17 00:00:00 2001 From: John Marshall Date: Fri, 14 Jul 2023 01:03:18 +1200 Subject: [PATCH 093/101] Don't run build-failures workflow on forked repositories (#41909) --- .github/workflows/build-failures.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build-failures.yml b/.github/workflows/build-failures.yml index 9376418841648..35b23b0eb1aa9 100644 --- a/.github/workflows/build-failures.yml +++ b/.github/workflows/build-failures.yml @@ -12,6 +12,7 @@ on: jobs: update-build-failure-page: name: Update build failure page + if: github.repository == 'bioconda/bioconda-recipes' runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 From b74b93fd6e66ff489918bb05f03226104b4507b3 Mon Sep 17 00:00:00 2001 From: Davy Cats Date: Thu, 13 Jul 2023 15:43:57 +0200 Subject: [PATCH 094/101] Add hmftools-neo (#41978) * Add hmftools-neo * fix copy-paste mistake --- recipes/hmftools-neo/build.sh | 12 ++++++ recipes/hmftools-neo/meta.yaml | 28 ++++++++++++++ recipes/hmftools-neo/neo.sh | 69 ++++++++++++++++++++++++++++++++++ 3 files changed, 109 insertions(+) create mode 100644 recipes/hmftools-neo/build.sh create mode 100644 recipes/hmftools-neo/meta.yaml create mode 100755 recipes/hmftools-neo/neo.sh diff --git a/recipes/hmftools-neo/build.sh b/recipes/hmftools-neo/build.sh new file mode 100644 index 0000000000000..c42a418b1ae3a --- /dev/null +++ b/recipes/hmftools-neo/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +[ -d "$TGT" ] || mkdir -p "$TGT" +[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" + +cd "${SRC_DIR}" +mv neo*.jar $TGT/neo.jar + +cp $RECIPE_DIR/neo.sh $TGT/neo +ln -s $TGT/neo $PREFIX/bin +chmod 0755 "${PREFIX}/bin/neo" diff --git a/recipes/hmftools-neo/meta.yaml b/recipes/hmftools-neo/meta.yaml new file mode 100644 index 0000000000000..496ee3a1d5a97 --- /dev/null +++ b/recipes/hmftools-neo/meta.yaml @@ -0,0 +1,28 @@ +{% set version = "1.0.1" %} +{% set sha256 = "292e322050965612c959296d11b45dcf9dba371d3c89d64bc10691116d867d90" %} + +package: + name: hmftools-neo + version: '{{ version }}' + +source: + url: https://github.com/hartwigmedical/hmftools/releases/download/neo-v{{ version }}/neo_v{{ version }}.jar + sha256: '{{ sha256 }}' + +build: + noarch: generic + number: 0 + +requirements: + run: + - openjdk >=8 + +test: + commands: + - 'neo 2>&1 | grep -q "Neo version"' + +about: + home: https://github.com/hartwigmedical/hmftools/tree/master/neo + license: GPL-3.0-only + license_family: GPL + summary: Identification of neoepitope and calculation of allele specific neoepitope binding and presentation likelihood. diff --git a/recipes/hmftools-neo/neo.sh b/recipes/hmftools-neo/neo.sh new file mode 100755 index 0000000000000..786a7a04f1dc5 --- /dev/null +++ b/recipes/hmftools-neo/neo.sh @@ -0,0 +1,69 @@ +#!/bin/bash +# hmftools neo executable shell script +# https://github.com/hartwigmedical/hmftools/tree/master/neo +set -eu -o pipefail + +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Java installed with Anaconda to ensure correct version +java="$ENV_PREFIX/bin/java" + +# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java" +if [ -n "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates' + then + pass_args="$arg" + else + pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg + fi + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == org\.* ]] || [[ ${pass_arr[0]:=} == com\.* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/neo.jar" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/neo.jar" $pass_args +fi +exit From 20c70c58ccf99dbc4c28d651c408ca9ece69d209 Mon Sep 17 00:00:00 2001 From: Davy Cats Date: Thu, 13 Jul 2023 15:44:22 +0200 Subject: [PATCH 095/101] Update hmftools-isofox to v1.6.2 (#41979) --- recipes/hmftools-isofox/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-isofox/meta.yaml b/recipes/hmftools-isofox/meta.yaml index b8ffd0dbff8ff..9cc47f9fe3d22 100644 --- a/recipes/hmftools-isofox/meta.yaml +++ b/recipes/hmftools-isofox/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.5" %} -{% set sha256 = "9f6d9723184b5ed669c42d3409dae797b3be891fa639a867a84cd41bdf4c5190" %} +{% set version = "1.6.2" %} +{% set sha256 = "b681b48f0a0fc31de30a0721c0094f294b1e8fe1fb567447b7bf153120981cd2" %} package: name: hmftools-isofox From 0778e84fcc5d59b74a9ce694103d010f97725863 Mon Sep 17 00:00:00 2001 From: pengSherryYel <32877803+pengSherryYel@users.noreply.github.com> Date: Thu, 13 Jul 2023 15:57:54 +0200 Subject: [PATCH 096/101] Add replidec (#41972) * upload replidec * modify name * debug merge test * debug merge test add noarch * debug merge test change url * debug import error * debug remove import * debug remove import * add pip install script * Update meta.yaml * Update meta.yaml --------- Co-authored-by: Devon Ryan --- recipes/replidec/meta.yaml | 49 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/replidec/meta.yaml diff --git a/recipes/replidec/meta.yaml b/recipes/replidec/meta.yaml new file mode 100644 index 0000000000000..08313f980cb90 --- /dev/null +++ b/recipes/replidec/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "Replidec" %} +{% set version = "0.3.1.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://files.pythonhosted.org/packages/31/2a/eb6b903693c8bfc74086ca72976d700b73e9990058b24daecc0435f49f41/{{ name }}-{{ version }}.tar.gz" + sha256: 9152f2fa410b8206a23f5af5ac94747c1e876a7b32ac67ec9bea8d9faa5bd5d4 + +build: + number: 0 + entry_points: + - Replidec=Replidec.Replidec_cmdline:main + script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" + noarch: python + +requirements: + host: + - python >=3.9 + - biopython + - numpy >=1.23.1 + - pip + run: + - python >=3.9 + - biopython + - numpy >=1.23.1 + - mmseqs2 + - blast + - hmmer + - prodigal + +test: + commands: + - Replidec --help + - python -m Replidec.Replidec_cmdline -h + requires: + - pip + +about: + home: "https://github.com/deng-lab/Replidec" + license: MIT + license_family: MIT + summary: "Replication Cycle Decipher for Phages" + +extra: + recipe-maintainers: + - pengSherryYel From 9aef91cfbbad9779ba078a007db5a5c4f2dd65c4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 13 Jul 2023 08:29:25 -0600 Subject: [PATCH 097/101] Update baltic to 0.2.2 (#41980) --- recipes/baltic/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/baltic/meta.yaml b/recipes/baltic/meta.yaml index 4d81e64812c2b..1838b30e463fb 100644 --- a/recipes/baltic/meta.yaml +++ b/recipes/baltic/meta.yaml @@ -1,5 +1,5 @@ {% set name = "baltic" %} -{% set version = "0.2.1" %} +{% set version = "0.2.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 7b942c0c6ff5b4ab8b6663191a9a874db6e2ff6b149f32b205011fbc6fc41602 + sha256: 095045aeb0f86f7668df5d7f163ab9fec30e59a564fc77c06b5cb756027a1e79 build: number: 0 From 2cb887e922c2260df51c50d74f1739251568368d Mon Sep 17 00:00:00 2001 From: Hamdiye Uzuner Date: Thu, 13 Jul 2023 16:30:30 +0200 Subject: [PATCH 098/101] Update arcasHLA requirements for scipy version (#41938) * Update version of samtools dependency to >=1.10 * set correct requirement for scipy version * update build number * add space before version number meta.yaml --------- Co-authored-by: David Laehnemann --- recipes/arcas-hla/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/arcas-hla/meta.yaml b/recipes/arcas-hla/meta.yaml index 65bffffe6ed09..6e4fb4048e5b5 100644 --- a/recipes/arcas-hla/meta.yaml +++ b/recipes/arcas-hla/meta.yaml @@ -9,7 +9,7 @@ source: sha256: fb17b3ba74facf4edb3329099b158910bdc7c4e73074efab9880d4136a0d4e93 build: - number: 1 + number: 2 noarch: generic requirements: @@ -25,7 +25,7 @@ requirements: - pigz - python >=3.6.1 - samtools >=1.9 - - scipy + - scipy ==1.1.0 test: commands: From d504224b1625227647a3aed76ce4355eaf6eb339 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 13 Jul 2023 09:17:04 -0600 Subject: [PATCH 099/101] Update gget to 0.27.8 (#41973) --- recipes/gget/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gget/meta.yaml b/recipes/gget/meta.yaml index 3a01e1ec2d3d0..d634c284a5a31 100644 --- a/recipes/gget/meta.yaml +++ b/recipes/gget/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gget" %} -{% set version = "0.27.7" %} -{% set sha256 = "b77410a6f8753dd8145ede556caac2609954721f0e1de2949db970bf0da31833" %} +{% set version = "0.27.8" %} +{% set sha256 = "40d31eb6f003ece6957747b510c038dda7665a490207b300c9762d94c96fff10" %} package: name: "{{ name|lower }}" From d2102a7727556571179109c4e6746b5e6109edab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 13 Jul 2023 21:42:44 +0200 Subject: [PATCH 100/101] add vcflib to freebayes run section (#41976) * add vcflib to run section * trigger rerun * trigger rerun --- recipes/freebayes/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/freebayes/meta.yaml b/recipes/freebayes/meta.yaml index 12b4e2c7deb0e..fbac60b01d1fe 100644 --- a/recipes/freebayes/meta.yaml +++ b/recipes/freebayes/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 6016c1e58fdf34a1f6f77b720dd8e12e13a127f7cbac9c747e47954561b437f5 build: - number: 5 + number: 6 skip: true # [osx] requirements: @@ -29,6 +29,7 @@ requirements: - parallel - samtools - tabixpp + - vcflib test: commands: From 9561bd6c8f650a1b33715657266af7450a76f646 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 14 Jul 2023 00:17:21 -0600 Subject: [PATCH 101/101] Update taxpasta to 0.4.1 (#41988) --- recipes/taxpasta/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxpasta/meta.yaml b/recipes/taxpasta/meta.yaml index 0595ea3dae406..7480ef4740dfa 100644 --- a/recipes/taxpasta/meta.yaml +++ b/recipes/taxpasta/meta.yaml @@ -1,6 +1,6 @@ {% set name = "taxpasta" %} -{% set version = "0.4.0" %} -{% set sha256 = "8a0c95478845c2a2c041083620c17b99dd3b085b8677f7dae3341b5bd6d8f2bf" %} +{% set version = "0.4.1" %} +{% set sha256 = "685839dbc90b4dc6eb153395a42c8128f8bf472b78f1f03c5a77849d4112b0d7" %} package: name: {{ name|lower }}