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I'm looking at the profile repositories for examples.
How does snakemake resolve the script paths: e.g. cluster: "grid-submit.py" (from {profiledir}/config.yaml)?
If I am to copy the profile directory in the same folder as a Snakefile, and use --profile {profiledir}, snakemake complains that grid-submit.py cannot be found. Are we expected to modify the config.yaml inside the profile to make script paths relative to the Snakefile?
Or is~/.config/snakemake treated specially?
The text was updated successfully, but these errors were encountered:
init-js
changed the title
Are the paths to the scripts inside config.yaml meant to be added to the PATH?
Are the paths to the scripts inside config.yaml meant to be added to $PATH?
Mar 22, 2018
I'm looking at the profile repositories for examples.
How does snakemake resolve the script paths: e.g.
cluster: "grid-submit.py"
(from{profiledir}/config.yaml
)?If I am to copy the profile directory in the same folder as a Snakefile, and use
--profile {profiledir}
, snakemake complains thatgrid-submit.py
cannot be found. Are we expected to modify the config.yaml inside the profile to make script paths relative to the Snakefile?Or is
~/.config/snakemake
treated specially?The text was updated successfully, but these errors were encountered: