fix conda in snakemake - Githubissues

nih-cfde / use-case-library-build

https://use-cases.nih-cfde.org/

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Closed ACharbonneau closed 3 years ago

ACharbonneau commented 3 years ago

did this on the wrong branch, but whatever.

changed Snakemake shell commands to use {python} instead of python, so that they use the conda envs properly.

ctb commented 3 years ago

could you also remove python=sys.executable pls?

ACharbonneau commented 3 years ago

doing that made it break, so I put it back

ctb commented 3 years ago

I think that's because you missed one {python}? see -

ctb commented 3 years ago

yep. That needs to be changed to, or all is for naught.

ACharbonneau commented 3 years ago

with line 8 deleted:

ACharbonneau commented 3 years ago

ahh

ACharbonneau commented 3 years ago

checked with line 8 deleted and all the pythons fixed and it works now.