Enable the use of containers when --use-conda is not defined #381
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replaces all conda envs with None if --use-conda is not set, so that it doesn't try to build the conda env using the container, and instead just simply use the container for execution.
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Note: this currently only works for snakemake>=8.0 (so python >= 3.11), should be able to fix this, just need to find out what variable the deployment mode is defined in for snakemake < 8.0 |
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actually there are also a couple container edits that were needed too, just testing those out, but if those work, make sure you use an updated container (e.g. delete your old one).. |
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ok this should be good to go now, tested with updated hippunfold-deps container, and added fix that works for older and newer snakemake versions |
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The issue was that whenever any rule has both a conda and container directive defined, then it checks the version of conda in the container, since the behaviour will be to use the container to build the conda env.
But for us, we just want the container to be used without conda at all, so this adds a wrapper when defining conda environments, so that it is set to
Noneif the--use-condaflag is not set.Looks to be working fine in dry-run, will do a full test now..