iam - matplotlib dependency

[kern3020]

I believe I got the installation correct(as documented) and clean. Yet, there was an additional dependency for iam

$ bcbio_vm.py aws iam
Traceback (most recent call last):
  File "/usr/local/bin/bcbio_vm.py", line 4, in <module>
    __import__('pkg_resources').run_script('bcbio-nextgen-vm==0.1.0a', 'bcbio_vm.py')
  File "/home/jkern/install/bcbio-vm/anaconda/lib/python2.7/site-packages/setuptools-7.0-py2.7.egg/pkg_resources.py", line 517, in run_script
  File "/home/jkern/install/bcbio-vm/anaconda/lib/python2.7/site-packages/setuptools-7.0-py2.7.egg/pkg_resources.py", line 1443, in run_script
  File "/home/jkern/install/bcbio-vm/anaconda/lib/python2.7/site-packages/bcbio_nextgen_vm-0.1.0a-py2.7.egg/EGG-INFO/scripts/bcbio_vm.py", line 22, in <module>

  File "/home/jkern/install/bcbio-vm/anaconda/lib/python2.7/site-packages/bcbio_nextgen_vm-0.1.0a-py2.7.egg/bcbiovm/graph/graph.py", line 6, in <module>
ImportError: No module named matplotlib

[kern3020]

iam facility is to setup users, groups and policy. To me this error is strange. Why does iam need a plotting library?

Aside: I am running this installation from a headless instance (ie, no GUI).

[chapmanb]

John;
Apologies, @jwm added in plotting capabilities to examine CPU/memory/network/disk resource usage during runs but I forgot to add the matplotlib conda dependency. I pushed a fix for the future but for your current installation doing:

/home/jkern/install/bcbio-vm/anaconda/bin/conda install matplotlib

should get it running again. To answer your question, plotting is not required here but you're just getting the error from pulling in the dependency via imports. Hopefully that addition will get you running again.

@jwm, I wonder if it would make sense to move this inside of bcbio-nextgen/docker to avoid the external matplotlib dependency. Then it could also run in an automated way at the end of a bcbio run. The challenge would be pulling in all the data from the compute* nodes but we could probably query SLURM or something to find out all of the names. What do you think?