MAF tools do not find indexed hg19 46-way or 100-way. CVMFS path problem?

[jennaj]

Found while retesting this fix: https://github.com/galaxyproject/usegalaxy-playbook/issues/130#issuecomment-595373150

Test history: https://usegalaxy.org/u/jen/h/test-maf-tools---tool-group-fetch-alignmentssequences

dataset 51: Fatal Error: The MAF source specified (46_WAY_MULTIZ_hg19) appears to be invalid. dataset 50: Fatal Error: The MAF source specified (100_WAY_MULTIZ_v2_hg19) appears to be invalid.

@natefoo @davebx - Paths in CVMFS changed. Maybe these were missed when others fixed?

[jennaj]

Related issues: https://github.com/search?q=org%3Agalaxyproject+maf&type=Issues

Many involve MAF tools, not just data. Some might be resolved, needs an update.

[natefoo]

My favorite construct: catch exceptions and silently ignore them.

Traceback (most recent call last):
  File "/home/ndc/maf_utilities.py", line 299, in maf_index_by_uid
    return bx.align.maf.MultiIndexed(maf_files, keep_open=True, parse_e_rows=False)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/bx/interval_index_file.py", line 175, in __init__
    for fname in filenames]
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/bx/interval_index_file.py", line 175, in <listcomp>
    for fname in filenames]
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/bx/interval_index_file.py", line 178, in new_indexed_access
    return self.indexed_access_class(data_filename, index_filename, keep_open, **kwargs)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/bx/interval_index_file.py", line 234, in __init__
    self.f = self.open_data()
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/bx/align/maf.py", line 47, in open_data
    return TextIOWrapper(data, encoding="ascii")
AttributeError: 'SeekableLzopFile' object has no attribute 'readable'

I think SeekableLzopFile needs to implement io.IOBase?

[mvdbeek]

Combined with lack of testing it's a thing of beauty!