cwltool conflict version?

Hi,

I’m trying to run a CWL workflow for bcbio-nextgen in our SLURM cluster using Toil. To do so, I’m running the following command: cwltoil --verbose --preserve-environment PATH HOME --no-container run_info-cwl-workflow/main-run_info-cwl.cwl run_info-cwl-workflow/main-run_info-cwl-samples.json.

The command is the same than the one specified in bcbio-nextgen docs, just that I use cwltoil instead of cwltool.

When doing so, I’m getting the following error:

 login01 /scratch/gcarrasco/tests/test_bcbio_cwl ~> cwltoil --verbose --preserve-environment PATH HOME --no-container run_info-cwl-workflow/main-run_info-cwl.cwl run_info-cwl-workflow/main-run_info-cwl-samples.json                        Traceback (most recent call last):
  File "/cm/shared/apps/bcbio/20150720-devel/data/anaconda/bin/cwltoil", line 9, in <module>
    load_entry_point('toil==3.2.0a2', 'console_scripts', 'cwltoil')()
  File "/cm/shared/apps/bcbio/20150720-devel/data/anaconda/lib/python2.7/site-packages/setuptools-20.2.2-py2.7.egg/pkg_resources/__init__.py", line 549, in load_entry_point
  File "/cm/shared/apps/bcbio/20150720-devel/data/anaconda/lib/python2.7/site-packages/setuptools-20.2.2-py2.7.egg/pkg_resources/__init__.py", line 2542, in load_entry_point
  File "/cm/shared/apps/bcbio/20150720-devel/data/anaconda/lib/python2.7/site-packages/setuptools-20.2.2-py2.7.egg/pkg_resources/__init__.py", line 2201, in load
  File "/cm/shared/apps/bcbio/20150720-devel/data/anaconda/lib/python2.7/site-packages/setuptools-20.2.2-py2.7.egg/pkg_resources/__init__.py", line 2218, in require
  File "/cm/shared/apps/bcbio/20150720-devel/data/anaconda/lib/python2.7/site-packages/setuptools-20.2.2-py2.7.egg/pkg_resources/__init__.py", line 835, in resolve
pkg_resources.VersionConflict: (cwltool 1.0.20160422204730 (/cm/shared/apps/bcbio/20150720-devel/data/anaconda/lib/python2.7/site-packages/cwltool-1.0.20160422204730-py2.7.egg), Requirement.parse('cwltool==1.0.20160413143011'))

Looking at the code I saw that the version of cwltool required is set in setup.py. Isn’t this a too strict requirement? I’d suggest changing it for

        'cwl': [
            'cwltool>=1.0]},

Ping @tetron 😃

[mr-c]

So yes, https://github.com/BD2KGenomics/toil/blob/master/setup.py#L43 should be changed to use a >= a known working version.

[hannes-ucsc]

Use of ‘>=’ version constraints are discouraged. See #827 for discussion.