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 diff --git a/build-fail-blacklist b/build-fail-blacklist index 626793dbd0200..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 @@ -835,9 +834,6 @@ 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 +885,6 @@ 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 +906,6 @@ 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/annonars/meta.yaml b/recipes/annonars/meta.yaml index 06279afd2d879..759db79c01021 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.12.7" %} +{% 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: 769a95422791f82132aef9154d98ab15b79797baf90b299ff1a358750fd951fb + sha256: 6e1869f4965bd096b60c386253f6a85879094ad50b01541c6df04f8225f87cdc requirements: build: 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: 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: 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" diff --git a/recipes/baltic/meta.yaml b/recipes/baltic/meta.yaml index 7b945b8ba9dc1..1838b30e463fb 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 = "0.2.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: e1a392b376b42861c4d33d92bce412ab92dc9b266f33949e83a78794de88d223 + sha256: 095045aeb0f86f7668df5d7f163ab9fec30e59a564fc77c06b5cb756027a1e79 build: number: 0 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: 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 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 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 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] 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 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 }} 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')" 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 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: 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 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 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 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: diff --git a/recipes/freebayes/meta.yaml b/recipes/freebayes/meta.yaml index e3f3489e24e82..fbac60b01d1fe 100644 --- a/recipes/freebayes/meta.yaml +++ b/recipes/freebayes/meta.yaml @@ -9,7 +9,8 @@ source: sha256: 6016c1e58fdf34a1f6f77b720dd8e12e13a127f7cbac9c747e47954561b437f5 build: - number: 4 + number: 6 + skip: true # [osx] requirements: build: @@ -23,12 +24,12 @@ requirements: - bzip2 - htslib - tabixpp + - vcflib run: - - htslib - parallel - samtools - - vcflib - tabixpp + - vcflib test: commands: 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 }}" 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 }}" 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: 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 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 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 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 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" diff --git a/recipes/hostile/meta.yaml b/recipes/hostile/meta.yaml new file mode 100644 index 0000000000000..4c894e0531464 --- /dev/null +++ b/recipes/hostile/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "0.0.3" %} + +package: + name: hostile + version: {{ version }} + +source: + url: https://pypi.io/packages/source/h/hostile/hostile-{{ version }}.tar.gz + sha256: efaef22a482cc7fab0217804f0112ac7795079cbbfb433cb0a2d0f456f8e16ac + +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 diff --git a/recipes/icount-mini/meta.yaml b/recipes/icount-mini/meta.yaml index 04da00261cd9c..e25f9f8c32e2a 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 = "3.0.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: eabda13cef86833eb9d3ce1e3edd3d99759149056f328f70aa0fbba1312c0107 + sha256: 795e2ee77c5a23c96c01d4144c5b78103982ec3aa7274fea8f3ed94c0fd511ac 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: 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: 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: 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 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 diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 242f6a0423352..1eeb3285291ad 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 }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: bb618eef74a23fd336b8e950ade5ecb65f1096d8ddfeced0e01934d20048557f + 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: diff --git a/recipes/mehari/meta.yaml b/recipes/mehari/meta.yaml index ffdc65aeefb57..64fb2b7207308 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 = "0.6.1" %} +{% set sha256 = "024598372c02ca2958465313a114494fcd9633e9a62292999b39984cef014064" %} package: name: mehari 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 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 $PREFIX -type f -name 'hg38*' -exec rm {} \; diff --git a/recipes/modle/build.sh b/recipes/modle/build.sh index 48989353034b5..af31fd2fb2785 100755 --- a/recipes/modle/build.sh +++ b/recipes/modle/build.sh @@ -17,15 +17,17 @@ export CONAN_HOME="$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)" 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: 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 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" 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 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: 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: 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 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: 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 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 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: diff --git a/recipes/pmx_biobb/meta.yaml b/recipes/pmx_biobb/meta.yaml index 8746c50713770..231ea0b39d417 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: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" @@ -24,13 +24,15 @@ requirements: - {{ compiler('fortran') }} - make host: - - python >=3.7 + - python =3.7 - setuptools - scipy - matplotlib-base - rdkit run: - - python >=3.7 + - boost-cpp + - cxx-compiler + - python =3.7 - scipy - matplotlib-base - rdkit 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 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 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__)" 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: 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 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 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: - - $R -e "library('InterpretMSSpectrum')" - -about: - home: http://dx.doi.org/10.1021/acs.analchem.6b02743 - license: GPL-3.0-only - summary: Annotate and interpret deconvoluted mass spectra (mass*intensity pairs) from high - resolution mass spectrometry devices. - license_family: GPL3 - license_file: - - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' diff --git a/recipes/r-mytai/build.sh b/recipes/r-mytai/build.sh new file mode 100644 index 0000000000000..e8fdcfec9c6d1 --- /dev/null +++ b/recipes/r-mytai/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash +export DISABLE_AUTOBREW=1 + +mv DESCRIPTION DESCRIPTION.old +grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION +# shellcheck disable=SC2086 +${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: + - $R -e "library('myTAI')" # [not win] + +about: + home: https://github.com/drostlab/myTAI + summary: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2017) ). The aim of this tool is to provide a transcriptome analysis environment to quantify the average evolutionary age of genes contributing to a transcriptome of interest (Drost et al. (2016) ). + license: GPLv3 + license_family: GPL + +extra: + recipe-maintainers: + - gallardoalba diff --git a/recipes/r-recetox-aplcms/meta.yaml b/recipes/r-recetox-aplcms/meta.yaml index 8f86685424f2a..a8506f6814e97 100644 --- a/recipes/r-recetox-aplcms/meta.yaml +++ b/recipes/r-recetox-aplcms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "recetox-aplcms" %} -{% set version = "0.11.0" %} +{% set version = "0.12.0" %} {% set github = "https://github.com/RECETOX" %} package: @@ -8,7 +8,7 @@ package: source: url: "{{ github }}/recetox-aplcms/archive/refs/tags/v{{ version }}.tar.gz" - sha256: e956f401bf75b5733111fd0316b2abe76ae93d6735a49aa58b864aad321555e6 + sha256: c76715e50a442b45f46f79120af6f382965f9a8de63bf0f624eb132478b6ed2c build: number: 0 diff --git a/recipes/r-wormbase/build.sh b/recipes/r-wormbase/build.sh new file mode 100644 index 0000000000000..5bf492ab9fc06 --- /dev/null +++ b/recipes/r-wormbase/build.sh @@ -0,0 +1 @@ +$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 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 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 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'] 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 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 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: 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 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 diff --git a/recipes/superdsm/meta.yaml b/recipes/superdsm/meta.yaml index 06cb204070a99..12aa1e1c73a4d 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" %} @@ -9,7 +9,7 @@ package: source: url: "{{ repo_url }}/archive/refs/tags/v{{ version }}.zip" - sha256: e00e13b9bb330fccc38fb46629b651d541a3ff66339c2b5d3d962811cf375c63 + sha256: f55abbd6818a66886ddfe3f7fd9c5dd93c63ed2b6e3179552106e560a000ad5f build: number: 1 @@ -27,14 +27,13 @@ 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 - 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: 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. 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 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: 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 }} 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 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 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 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: 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: 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: 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: 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/$=3 - - cmake - - pkg-config host: + - libgomp # [linux] + - llvm-openmp # [osx] + - zlib - htslib - tabixpp + - pkg-config + - wfa2-lib run: - python >=3 - - zlib + - perl - htslib - tabixpp + - eigen + - jsoncpp + - wfa2-lib + test: commands: - - vcfallelicprimitives -h - - vcffirstheader < /dev/null - - vcfsort < /dev/null - - vcfrandom | grep 'fileformat=VCF' + - "vcfwave -h" + - "vcffirstheader < /dev/null" + - "vcfsort < /dev/null" about: home: https://github.com/vcflib/vcflib @@ -48,4 +67,4 @@ about: extra: identifiers: - biotools:vcflib - - doi:10.1101/023754 + - doi:10.1371/journal.pcbi.1009123 diff --git a/recipes/vcflib/pkg-config.patch b/recipes/vcflib/pkg-config.patch index 10ffa242b87c6..ae58978242cc2 100644 --- a/recipes/vcflib/pkg-config.patch +++ b/recipes/vcflib/pkg-config.patch @@ -1,8 +1,8 @@ Author: Andreas Tille modified for bioconda by Jon Puritz Description: Add pkg-config file to simplify building of freebayes Forwarded: not-needed ---- /dev/null -+++ libvcflib/libvcflib.pc +--- a/dev/null ++++ b/libvcflib/libvcflib.pc @@ -0,0 +1,12 @@ +prefix=/usr +exec_prefix=${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 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 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" 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: 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 diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index 08b6d2b83410c..670bc4bd49e89 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 = "1.3.6" %} 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: a97b6ccd94909a11aacc4b6d2474dc02dabcf93da0693f239138c5c52f781518 + sha256: 7a7dc68fd2b119a49e19a825fedd889fd167693b514fc29fcc4e0be3c7fa6706 build: number: 0 @@ -51,6 +51,7 @@ requirements: - slclust - trimal - gzip + - miniprot =0.7 test: commands: