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As you can see, the environment variables are quoted as a group which makes bash crash.
Additional context
The issue seems to be the usage of AlwaysQuotedFormatter in snakemake.utils when calling format for the job script with _quote_all=True. Changing this to _quote_all=False fixed the issue for me, but I am not sure if this breaks other cases.
The text was updated successfully, but these errors were encountered:
This seems to be loosely connected to #1007 in that it also involves quoting of environment variables (see also #1008). Rather than disabling _quote_all entirely I have circumvented this by manually prepending envvars to exec_job rather than letting format_job() handle it in
First of all, sorry for the late response. After many new features, Snakemake is approaching feature completeness (at least for my personal agenda and at the moment). Hence, now is the time to fix or close all the open bugs.
Above PR provides a fix on a kind of global scale. Thanks a lot for pointing to the issue!
Snakemake version
v5.32.0
Describe the bug
When using the
envvars
directive, submitting jobs on a cluster will fail with[list of env. vars] is not a command
.Minimal example
Consider this Snakefile:
This will generate a job script of this form
As you can see, the environment variables are quoted as a group which makes bash crash.
Additional context
The issue seems to be the usage of
AlwaysQuotedFormatter
insnakemake.utils
when callingformat
for the job script with_quote_all=True
. Changing this to_quote_all=False
fixed the issue for me, but I am not sure if this breaks other cases.The text was updated successfully, but these errors were encountered: