cwl for H3Bionet16S on Ubuntu 16.04.1 failing

Question

[Shakuntala Baichoo]

I am running the H3aBionet16S pipeline on a linux vm 16.04.1 LTS (Xenial Xerus) with correct Node.js i.e. v4.2.6 and cwl version 1.0.20160907111242, but when I run the pipeline as follows:

(qiime1) sbaichoo@sbaichoo-virtual-machine:/home/user/h3abionet16S/example$ sudo cwltool --debug --cachedir /scratch/user/h3abionet16S/cachedir/cache --outdir /scratch/user/h3abionet16S/workflow_output /home/user/h3abionet16S/workflows/completeWorkflow.cwl /home/user/h3abionet16S/example/input.yml

I am getting the following error:

Traceback (most recent call last):
      File "/usr/local/bin/cwltool", line 5, in <module>
        from pkg_resources import load_entry_point
      File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 2927, in <module>
        @_call_aside
      File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 2913, in _call_aside
        f(*args, **kwargs)
      File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 2940, in _initialize_master_working_set
        working_set = WorkingSet._build_master()
      File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 637, in _build_master
        return cls._build_from_requirements(__requires__)
      File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 650, in _build_from_requirements
        dists = ws.resolve(reqs, Environment())
      File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 829, in resolve
        raise DistributionNotFound(req, requirers)
    pkg_resources.DistributionNotFound: The 'html5lib<=0.9999999,>=0.90' distribution was not found and is required by schema-salad

Grateful if I could get a solution to this problem. Thank you.

[Shakuntala Baichoo]

It's ok got the solution. The following does not work.

sudo /usr/bin/pip install cwltool

It does not install all dependencies especially the correct version of html5lib. Had to re-install cwl using git source