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Incompatibility with snakemake>8 #33

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2 tasks done
votti opened this issue Apr 15, 2024 · 0 comments
Open
2 tasks done

Incompatibility with snakemake>8 #33

votti opened this issue Apr 15, 2024 · 0 comments

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@votti
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votti commented Apr 15, 2024

Have you already done this?

Environment

  • setup environment with: mamba create -n drop_env_debug -c conda-forge -c bioconda drop --override-channels
name: drop_env_debug
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
...
  - python=3.12.2=hab00c5b_0_cpython
 ...
  - snakemake-interface-common=1.17.2=pyhdfd78af_0
  - snakemake-interface-executor-plugins=9.1.1=pyhdfd78af_0
  - snakemake-interface-report-plugins=1.0.0=pyhdfd78af_0
  - snakemake-interface-storage-plugins=3.1.1=pyhdfd78af_0
  - snakemake-minimal=8.10.7=pyhdfd78af_0
...
  - wbuild=1.8.0=pyhdfd78af_1

Issue description

Runing as wbuild wirjfkiw with snakemake>=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`

  1. 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
  1. 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>

@votti votti changed the title Incompatibility with snakemake>8 (get_argument_parser Incompatibility with snakemake>8 Apr 15, 2024
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