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Plastid dependency pysam needs to be pinned #12494

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lparsons opened this issue Dec 5, 2018 · 0 comments · Fixed by #15775
Closed

Plastid dependency pysam needs to be pinned #12494

lparsons opened this issue Dec 5, 2018 · 0 comments · Fixed by #15775

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@lparsons
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lparsons commented Dec 5, 2018

After installing plastid, I get the following error trying to run counts_in_region -h:

Traceback (most recent call last):
  File "/home/lparsons/miniconda3/envs/plastid/bin/counts_in_region", line 11, in <module>
    load_entry_point('plastid==0.4.8', 'console_scripts', 'counts_in_region')()
  File "/home/lparsons/miniconda3/envs/plastid/lib/python3.6/site-packages/pkg_resources/__init__.py", line 487, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/home/lparsons/miniconda3/envs/plastid/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2728, in load_entry_point
    return ep.load()
  File "/home/lparsons/miniconda3/envs/plastid/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2346, in load
    return self.resolve()
  File "/home/lparsons/miniconda3/envs/plastid/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2352, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/home/lparsons/miniconda3/envs/plastid/lib/python3.6/site-packages/plastid/__init__.py", line 44, in <module>
    from plastid.genomics.genome_array import (BAMGenomeArray,
  File "/home/lparsons/miniconda3/envs/plastid/lib/python3.6/site-packages/plastid/genomics/genome_array.py", line 215, in <module>
    from plastid.genomics.map_factories import *
  File "libchtslib.pxd", line 2590, in init plastid.genomics.map_factories
ValueError: pysam.libchtslib.HTSFile has the wrong size, try recompiling. Expected 88, got 80

Potentially need to pin pysam in the run block using - {{ pin_compatible('pysam') }}. @bgruening Does this work for packages other than numpy? What determines the "compatible" versions?

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