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cgat-apps repository
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module 'cgatcore.experiment' has no attribute 'ArgumentParser' #63

Closed IanSudbery closed 4 years ago

IanSudbery commented 4 years ago

From a user on biostars:

Thanks very much for this! However, I'm struggling to find documentation on the gtf2gtf tool in cgat, and in particular the flags that the tool accepts. --help gives an error:
cgat gtf2gtf --help Traceback (most recent call last): 
  File "/home/oates_binf_1/software/miniconda3/bin/cgat", line 11, in <module> sys.exit(main()) 
  File "/home/oates_binf_1/software/miniconda3/lib/python3.7/site-packages/cgat/cgat.py", line 132, in main module.main(sys.argv) 
  File "/home/oates_binf_1/software/miniconda3/lib/python3.7/site-packages/cgat/tools/gtf2gtf.py", line 362, in main parser = E.ArgumentParser(description=__doc__) 
AttributeError: module 'cgatcore.experiment' has no attribute 'ArgumentParser'

From someone that has just done conda install -c bioconda cgat-apps

https://www.biostars.org/p/426276/#426468

Is this another casualty of switching from ArgumentParser to OptionParser?

Is there a version mismatch between cgatcore and cgat-apps?

IanSudbery commented 4 years ago

Actaully, I can't find cgat-core listed as a requirement anywhere, let alone the version?

Acribbs commented 4 years ago

I think this may because the software is defaulting to an older version of cgatcore. I will fix the Conda recipe to specify the latest version of cgatcore==0.6.5

Acribbs commented 4 years ago

FYI latest version of cgatcore can handle both Argparse and Optparse

Acribbs commented 4 years ago

please see https://github.com/bioconda/bioconda-recipes/pull/20822