Update the snakemake pipeline to run tierpsy tracker and begin documentation of pipeline in README #6
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keithchev
approved these changes
Sep 19, 2024
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| -e SHELL=/bin/bash \ | ||
| -e HOME=/home/tierpsy_user \ | ||
| -e PATH=/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/tierpsy_user/.local/bin \ | ||
| -e TERM=xterm \ | ||
| -e PWD=/DATA \ | ||
| -e SHLVL=1 \ | ||
| -e LIBGL_ALWAYS_INDIRECT=1 \ | ||
| -e DOCKER_HOME=/home/tierpsy_user \ |
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Is it possible to set some of these env vars in the dockerfile instead? That would de-clutter the snakefile a bit (and clarify which env vars don't need to be specific to this docker exec command).
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I do not know how to do that, so I'll open an issue for this as well!
Edit: see #11
Co-authored-by: Keith Cheveralls <[email protected]> Signed-off-by: Taylor Reiter <[email protected]>
This was referenced Sep 20, 2024
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PR checklist
Fixes #123, Resolves #456).condaenvironments.Issues
Description
This PR adds a rule to run Tierpsy tracker to the snakefile. It includes instructions/documentation for Docker. I'm fully aware that this is a sub-par solution, but I think it's good enough for now.
I also started documented the pipeline in the README. I'll add more in future PRs.