use of conda has us approaching file limits

[aleighbrown]

We should make a docker env for our pipeline (or for each workflow) and run in those instead

[SamBryce-Smith]

We should try to use the --cleanup-conda-envs option (or the option along those lines) to try to remove the junk environments. But since most rules just involve running a single tool at a time, we can just use the Dockerfiles produced by the Biocontainers project to run the tools. Less work for us, also saves us the hassle of maintaining/making our own monstrosity of a Docker image...

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On Wed, 18 Jan 2023, 11:42 Anna-Leigh Brown, ***@***.***> wrote: We should make a docker env for our pipeline (or for each workflow) and run in those instead — Reply to this email directly, view it on GitHub <#55>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AL5JYDV74T4MMT25XZNUFDDWS7JJTANCNFSM6AAAAAAT67HHFA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[SamBryce-Smith]

--conda-cleanup-envs is what I meant, wrong way around... https://snakemake.readthedocs.io/en/stable/executing/cli.html