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Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)
http://moonso.github.io/genmod/
MIT License
74 stars 18 forks source link

container broken for version 3.8 #115

Closed jemten closed 9 months ago

jemten commented 9 months ago

Hello, The version 3.8 release of genmod on conda seems to be broken. It would be great to pin down the version numbers of everything. I install using conda install genmod=3.8 and run:

θ68° [anders.jemt@hasta:~/scripts]└2 [D_genmod_AJ] 5s $ genmod -v annotate --annotate-regions --genome-build 37 --outfile test.vcf /home/proj/stage/rare-
disease/cases/justhusky/analysis/justhusky/vcfparser_ar/justhusky_gatkcomb_rhocall_norm_af_mt_frqf_cadd_vep_parsed.19_selected.vcf
Traceback (most recent call last):
  File "/home/proj/stage/bin/miniconda3/envs/D_genmod_AJ/bin/genmod", line 10, in <module>
    sys.exit(cli())
  File "/home/proj/stage/bin/miniconda3/envs/D_genmod_AJ/lib/python3.10/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/proj/stage/bin/miniconda3/envs/D_genmod_AJ/lib/python3.10/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/proj/stage/bin/miniconda3/envs/D_genmod_AJ/lib/python3.10/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/proj/stage/bin/miniconda3/envs/D_genmod_AJ/lib/python3.10/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/proj/stage/bin/miniconda3/envs/D_genmod_AJ/lib/python3.10/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/home/proj/stage/bin/miniconda3/envs/D_genmod_AJ/lib/python3.10/site-packages/click/decorators.py", line 17, in new_func
    return f(get_current_context(), *args, **kwargs)
TypeError: annotate() got an unexpected keyword argument 'regions'
θ68° [anders.jemt@hasta:~/scripts]└2 [D_genmod_AJ] 4s 1 $ genmod --version
genmod version: 3.8.0

Also since the biocontainer image is based on the conda package it is broken there as well.

It is solvable by first installing genmod and then installing click version 8 so the problem seems to be with the click package specified in the requirements.txt

torbjorgen commented 9 months ago

@jemten solved click issue by:

RUN mamba install -y -c conda-forge -c bioconda python=3.8 pip pytabix=0.1 && \
    /opt/conda/bin/conda clean -ya && \
    pip install --no-cache-dir genmod==3.8.0 && \
    pip install --no-cache-dir click==8.1.3
torbjorgen commented 9 months ago

I uplifted the setup.py dependencies and now running the same command you used for testing in CI suite @jemten .