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Incompatible with `Snakemake>=8`
Currently drop
seems incompatible with the most recent Snakemake
version.
Reproducible issue
- Install
drop
:mamba create -n drop_env_debug -c conda-forge -c bioconda drop --override-channels
- Move to a drop envrionment (eg the demo one)
- Run
snakemake -n
or any othersnakemake
command
Error:
:~/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>
Workaround
Restrict snakemake
version during installation:
mamba create -n drop_env -c conda-forge -c bioconda drop snakemake-minimal=7.32 --override-channels
Mitigation
- Change example installation command.
- Specify dependency in
drop
conda release - This seems to be a
wbuild
issue and I will open add an issue there as well.
many thanks! we're fixing this and let you know once it's done