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mamba create -n drop_env -c conda-forge -c bioconda drop --override-channels
conda activate drop_env
mkdir ~/drop_demo
cd ~/drop_demo
drop demo
snakemake -n # dryrun
What's the expected result?
Workflow should work
What's the actual result?
Error:
(drop_env_debug) xxx:~/drop_demo$ snakemake -n
ImportError in file /home/vitoz/drop_demo/Snakefile, line 3:
cannot import name 'get_argument_parser' from 'snakemake' (/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/snakemake/__init__.py)
File "/home/vitoz/drop_demo/Snakefile", line 3, in <module>
File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/drop/__init__.py", line 1, in <module>
File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/drop/setupDrop.py", line 2, in <module>
File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/drop/config/__init__.py", line 1, in <module>
File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/drop/config/DropConfig.py", line 1, in <module>
File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/drop/config/SampleAnnotation.py", line 1, in <module>
File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/drop/utils.py", line 3, in <module>
File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/wbuild/__init__.py", line 10, in <module>
File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/wbuild/autolink.py", line 6, in <module>
File "/home/vitoz/mambaforge/envs/drop_env_debug/lib/python3.12/site-packages/wbuild/utils.py", line 12, in <module>
The text was updated successfully, but these errors were encountered:
votti
changed the title
Incompatibility with snakemake>8 (get_argument_parser
Incompatibility with snakemake>8Apr 15, 2024
Have you already done this?
Environment
mamba create -n drop_env_debug -c conda-forge -c bioconda drop --override-channels
Issue description
Runing as
wbuild
wirjfkiw withsnakemake>=8
fails as eg'get_argument_parser'
has been deprecated (Eg removal in commit: snakemake/snakemake@c9eaa4e#diff-f36ddf38d7a01c55552d675c82a06d201bd48a90ef14f916df328a2113ed66b6)Steps to reproduce the issue
I encountered this in the
drop
pipeline demo (https://github.com/gagneurlab/drop/issues/534`mamba create -n drop_env -c conda-forge -c bioconda drop --override-channels
snakemake -n # dryrun
What's the expected result?
Workflow should work
What's the actual result?
Error:
The text was updated successfully, but these errors were encountered: