Peter Van Dyken pvandyken
pvandyken
/ tmpdir_envvar.smk
Last active
July 22, 2022 17:49
Use an environment variable as the default resources tmpdir in a snakemake workflow
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| # For a local instance, use --default_resources 'tmpdir="$MYENV_VAR"' | |
| # Everything should work properly | |
| # For a cluster scheduling instance, use --default_resources 'tmpdir="$$MYENV_VAR"' | |
| # The double dollar sign is needed for escaping. | |
| # Note that you won't be able to use this tmpdir on localrules (only a concern in cluster mode) | |
| # The `tmpdir` variable becomes available for use throughout the workflow | |
| def eval_environ(s): |