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cgat-developers / cgat-apps

cgat-apps repository
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missing sortedcontainers module #42

Closed Acribbs closed 5 years ago

Acribbs commented 5 years ago

It seems that when you install cgat-apps from conda it is missing the sortedcontainers module.

It is within the yml file but isnt picked up in the environment. Is this a conda issue or something to do with cgat-apps yml?

Acribbs commented 5 years ago

Actually @sebastian-luna-valero I see sortedcontainers isn't actually missing in the conda recipe, its just not being picked up when installed

Acribbs commented 5 years ago

When running conda install sortedcontainers python 3.6 cgat-apps works, but python 3.7 doesn't with the following error:

  File "/ifs/devel/adamc/cgat-developers/conda-install/envs/cgat-apps-test/bin/cgat", line 11, in <module>
    sys.exit(main())
  File "/ifs/devel/adamc/cgat-developers/cgat-apps/cgat/cgat.py", line 129, in main
    module = imp.load_module(command, file, pathname, description)
  File "/ifs/devel/adamc/cgat-developers/conda-install/envs/cgat-apps-test/lib/python3.7/imp.py", line 234, in load_module
    return load_source(name, filename, file)
  File "/ifs/devel/adamc/cgat-developers/conda-install/envs/cgat-apps-test/lib/python3.7/imp.py", line 171, in load_source
    module = _load(spec)
  File "<frozen importlib._bootstrap>", line 696, in _load
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/ifs/devel/adamc/cgat-developers/cgat-apps/cgat/tools/bam2bam.py", line 155, in <module>
    from cgat.BamTools.bamtools import bam2bam_filter_bam, SetNH
ModuleNotFoundError: No module named 'cgat.BamTools.bamtools'