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make a note about how to use the docker containers in podman and galaxy #83

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merged 5 commits into from
Sep 27, 2023
Merged

make a note about how to use the docker containers in podman and galaxy #83

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c86c06a
initial testing galaxy version
exaexa Sep 26, 2023
3f712f8
docker: add all executables for all dockers
exaexa Sep 27, 2023
2707a2b
add SCIP to solvers in runfrog
exaexa Sep 27, 2023
23c522b
add note about running in galaxy and podman
exaexa Sep 27, 2023
4e454af
add temporary documenter compat
exaexa Sep 27, 2023
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7 changes: 7 additions & 0 deletions README.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion docker/Dockerfile.comparefrog
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Expand Up @@ -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()'

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1 change: 1 addition & 0 deletions docker/Dockerfile.generic
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Expand Up @@ -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()'

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4 changes: 2 additions & 2 deletions docker/Dockerfile.runfrog
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Expand Up @@ -2,8 +2,8 @@ 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()'
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"]
3 changes: 3 additions & 0 deletions docs/Project.toml
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@@ -1,2 +1,5 @@
[deps]
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

[compat]
Documenter = "<1"
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