feat: experimental podman support #227
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| @@ -5,9 +5,10 @@ hash_length: 7 | |||
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| # Specify the container framework used by each PRM wrapper. Valid options include: | |||
| # - docker (default if not specified) | |||
| # - podman - rootless version of docker, which should be a simple swap - if any algorithm doesn't work with podman, that is a bug. | |||
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is it a bug with SPRAS or with the algorithm itself?
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(Honestly, I don't expect that error to ever pop up, as the compatibility layer that Podman supplies is really robust)
This would usually be a problem with the algorithm, if it does use some weird quirk only available on docker, but I am unaware of any existing.
| # - singularity -- Also known as apptainer, useful in HPC/HTC environments where docker isn't allowed | ||
| # - dsub -- experimental with limited support, used for running on Google Cloud | ||
| container_framework: docker |
| @@ -5,6 +5,7 @@ dependencies: | |||
| - adjusttext=0.7.3.1 | |||
| - bioconda::snakemake-minimal=8.17.0 | |||
| - docker-py=5.0 | |||
| - podman=5.4.0 | |||
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should this also be 5.4.0.1?
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I ran into an issue when I pinned it to 5.4.0.1 and ignored it - I could look more into it, though I'll circle back to this PR since I figured out what was blocking me in the NetMix2 integration.
| @@ -239,6 +242,40 @@ def run_container_docker(container: str, command: List[str], volumes: List[Tuple | |||
| # finally: | |||
| return out | |||
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| # TODO any issue with creating a new client each time inside this function? | |||
| def run_container_podman(container: str, command: List[str], volumes: List[Tuple[PurePath, PurePath]], working_dir: str, environment: str = 'SPRAS=True'): | |||
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To test the Podman functionality, a test case should be added to each algorithm test (similar to the singularity test cases).
no formal test cases yet.
Closes #124