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Snakemake version
snakemake 7.12.0, 7.26.0 and 7.32.4
Describe the bug
When running a snakemake pipeline inside conda environment A , which contains a rule that works with a named conda environment B and a python script, the script is run using the wrong version of python. The environment B is activated, but the script is run with the python of environment A.
Logs
/path/to/environmentA/bin/python3.9 /.snakemake/scripts/tmp5edxuvzv.scriptname.py
Activating conda environment: B
Traceback (most recent call last):
File "/path/to/environmentA/bin/python3.9 /.snakemake/scripts/tmp5edxuvzv.scriptname.py", line 5, in <module>
ModuleNotFoundError: No module named 'package from environment B'
minimal example
create two named environments, one that includes snakemake version e.g 7.12.0 (A) , one other that includes a package B (B)
include python file that loads package B (B.py)
create snakemake file including
rule R:
conda: B
script:B.py
This will fail because it can not find package B inside environment B, the environment does not seem to be activated correctly
Additional context
This problem only occurs when running python scripts with a named Conda environment. Is a YAML file used instead, this problem does not occur. I had this problem with all mentioned snakemake versions.
The text was updated successfully, but these errors were encountered:
Snakemake version
snakemake 7.12.0, 7.26.0 and 7.32.4
Describe the bug
When running a snakemake pipeline inside conda environment A , which contains a rule that works with a named conda environment B and a python script, the script is run using the wrong version of python. The environment B is activated, but the script is run with the python of environment A.
Logs
minimal example
This will fail because it can not find package B inside environment B, the environment does not seem to be activated correctly
Additional context
This problem only occurs when running python scripts with a named Conda environment. Is a YAML file used instead, this problem does not occur. I had this problem with all mentioned snakemake versions.
The text was updated successfully, but these errors were encountered: