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Update shell prefix command in master.smk #1

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emi80 opened this issue Jul 25, 2022 · 0 comments
Open

Update shell prefix command in master.smk #1

emi80 opened this issue Jul 25, 2022 · 0 comments

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@emi80
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emi80 commented Jul 25, 2022

I think the shell.prefix definition in master.smk would need to be updated:

  • loading .bashrc is not needed most of the times
  • deactivating the active conda environment can give problems (e.g. missing binaries)

Something like:

shell.prefix('set -euo pipefail; export PATH="$PWD/LyRic/utils/:$PATH";')

should probably be fine.
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