From c86c06a0659b93e97500128bc508ad5f149c208a Mon Sep 17 00:00:00 2001 From: Mirek Kratochvil Date: Tue, 26 Sep 2023 23:31:28 +0200 Subject: [PATCH 1/5] initial testing galaxy version --- galaxy/FBCModelTestsFROG.xml | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 galaxy/FBCModelTestsFROG.xml diff --git a/galaxy/FBCModelTestsFROG.xml b/galaxy/FBCModelTestsFROG.xml new file mode 100644 index 0000000..9624126 --- /dev/null +++ b/galaxy/FBCModelTestsFROG.xml @@ -0,0 +1,21 @@ + + FROG reproducibility report generator + docker run -ti --rm -v \$PWD:/data -w /data ghcr.io/lcsb-biocore/docker/fbcmodeltests-run-frog -s GLPK '${model_xml}' generated_report + + + + + + + + + + + + + + +This tool creates a FROG reproducibility report from a constraint-based model stored in SBML FBC format. + + + From 3f712f8ecb804d1af03c51e57acdc311db98b766 Mon Sep 17 00:00:00 2001 From: Mirek Kratochvil Date: Wed, 27 Sep 2023 10:52:08 +0200 Subject: [PATCH 2/5] docker: add all executables for all dockers (they weightn't nothin') --- docker/Dockerfile.comparefrog | 2 +- docker/Dockerfile.generic | 1 + docker/Dockerfile.runfrog | 2 +- galaxy/FBCModelTestsFROG.xml | 21 --------------------- 4 files changed, 3 insertions(+), 23 deletions(-) delete mode 100644 galaxy/FBCModelTestsFROG.xml diff --git a/docker/Dockerfile.comparefrog b/docker/Dockerfile.comparefrog index adb0833..43eedf7 100644 --- a/docker/Dockerfile.comparefrog +++ b/docker/Dockerfile.comparefrog @@ -2,7 +2,7 @@ FROM julia ADD README.md Project.toml LICENSE /pkg/ ADD src/ /pkg/src/ -ADD bin/fbcmt-compare-frog /usr/bin +ADD bin/ /usr/bin/ RUN julia -e 'import Pkg; Pkg.develop(path="/pkg/"); Pkg.resolve(); Pkg.status(); Pkg.instantiate(); Pkg.precompile()' diff --git a/docker/Dockerfile.generic b/docker/Dockerfile.generic index 718e6f6..d67daa2 100644 --- a/docker/Dockerfile.generic +++ b/docker/Dockerfile.generic @@ -2,6 +2,7 @@ FROM julia ADD README.md Project.toml LICENSE /pkg/ ADD src/ /pkg/src/ +ADD bin/ /usr/bin/ RUN julia -e 'import Pkg; Pkg.develop(path="/pkg/"); Pkg.resolve(); Pkg.status(); Pkg.instantiate(); Pkg.precompile()' diff --git a/docker/Dockerfile.runfrog b/docker/Dockerfile.runfrog index 9269784..5d79454 100644 --- a/docker/Dockerfile.runfrog +++ b/docker/Dockerfile.runfrog @@ -2,7 +2,7 @@ FROM julia ADD README.md Project.toml LICENSE /pkg/ ADD src/ /pkg/src/ -ADD bin/fbcmt-run-frog /usr/bin +ADD bin/ /usr/bin/ RUN julia -e 'import Pkg; Pkg.add(["GLPK", "Tulip", "Clarabel", "OSQP", "Clp"]); Pkg.develop(path="/pkg/"); Pkg.resolve(); Pkg.status(); Pkg.instantiate(); Pkg.precompile()' diff --git a/galaxy/FBCModelTestsFROG.xml b/galaxy/FBCModelTestsFROG.xml deleted file mode 100644 index 9624126..0000000 --- a/galaxy/FBCModelTestsFROG.xml +++ /dev/null @@ -1,21 +0,0 @@ - - FROG reproducibility report generator - docker run -ti --rm -v \$PWD:/data -w /data ghcr.io/lcsb-biocore/docker/fbcmodeltests-run-frog -s GLPK '${model_xml}' generated_report - - - - - - - - - - - - - - -This tool creates a FROG reproducibility report from a constraint-based model stored in SBML FBC format. - - - From 2707a2b7a398c8c6cd5f245b5500a1757ab3dd9c Mon Sep 17 00:00:00 2001 From: Mirek Kratochvil Date: Wed, 27 Sep 2023 10:52:46 +0200 Subject: [PATCH 3/5] add SCIP to solvers in runfrog (it's GOOD) --- docker/Dockerfile.runfrog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/Dockerfile.runfrog b/docker/Dockerfile.runfrog index 5d79454..47690f4 100644 --- a/docker/Dockerfile.runfrog +++ b/docker/Dockerfile.runfrog @@ -4,6 +4,6 @@ ADD README.md Project.toml LICENSE /pkg/ ADD src/ /pkg/src/ ADD bin/ /usr/bin/ -RUN julia -e 'import Pkg; Pkg.add(["GLPK", "Tulip", "Clarabel", "OSQP", "Clp"]); Pkg.develop(path="/pkg/"); Pkg.resolve(); Pkg.status(); Pkg.instantiate(); Pkg.precompile()' +RUN julia -e 'import Pkg; Pkg.add(["GLPK", "Tulip", "Clarabel", "OSQP", "Clp", "SCIP"]); Pkg.develop(path="/pkg/"); Pkg.resolve(); Pkg.status(); Pkg.instantiate(); Pkg.precompile()' ENTRYPOINT ["/usr/bin/fbcmt-run-frog"] From 23c522ba4eec9ce319c7a6c773ea158dd278f1dc Mon Sep 17 00:00:00 2001 From: Mirek Kratochvil Date: Wed, 27 Sep 2023 10:58:25 +0200 Subject: [PATCH 4/5] add note about running in galaxy and podman --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/README.md b/README.md index 0e3f134..495d669 100644 --- a/README.md +++ b/README.md @@ -61,6 +61,13 @@ $ docker run -ti --rm -v $PWD:/data -w /data ghcr.io/lcsb-biocore/docker/fbcmode $ docker run -ti --rm -v $PWD:/data -w /data ghcr.io/lcsb-biocore/docker/fbcmodeltests-compare-frog report_dir other_dir ``` +Docker containers may be re-used and executed in many other environments: using +[podman](https://podman.io/) allows you to run in without installation in some +HPC setups; using the [Dockerized tool +capability](https://training.galaxyproject.org/training-material/topics/admin/tutorials/galaxy-docker/slides-plain.html) +of [Galaxy](https://usegalaxy.org/) allows you to run the model tests in many +institutional cloud-computing services and local Galaxy instances. + ## MEMOTE-style tests The primary entry point for the [MEMOTE](https://memote.readthedocs.io/) test From 4e454af5f090b60528783e07c8be20d53cbd5080 Mon Sep 17 00:00:00 2001 From: Mirek Kratochvil Date: Wed, 27 Sep 2023 11:11:50 +0200 Subject: [PATCH 5/5] add temporary documenter compat --- docs/Project.toml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/Project.toml b/docs/Project.toml index dfa65cd..32d0d89 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,2 +1,5 @@ [deps] Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" + +[compat] +Documenter = "<1"