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bcbio / bcbio-nextgen-vm

Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines
MIT License
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Typo in bcbiovm/aws/common.py prevents starting a cluster #162

Closed DavidQuigley closed 7 years ago

DavidQuigley commented 7 years ago

As of 5/1/2016, installing from Miniconda2 as directed in the cloud documentation.

Problem:

Running bcbio_vm.py aws cluster start throws a NameError exception: NameError: global name 'ansible_utils' is not defined

The traceback is:

Traceback (most recent call last):
  File "/usr/local/bin/bcbio_vm.py", line 4, in <module>
    __import__('pkg_resources').run_script('bcbio-nextgen-vm==0.1.0a0', 'bcbio_vm.py')
  File "/home/ubuntu/install/bcbio-vm/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 744, in run_script
  File "/home/ubuntu/install/bcbio-vm/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 1506, in run_script
  File "/home/ubuntu/install/bcbio-vm/anaconda/lib/python2.7/site-packages/bcbio_nextgen_vm-0.1.0a0-py2.7.egg/EGG-INFO/scripts/bcbio_vm.py", line 322, in <module>

  File "build/bdist.linux-x86_64/egg/bcbiovm/aws/cluster.py", line 120, in start
  File "build/bdist.linux-x86_64/egg/bcbiovm/aws/cluster.py", line 73, in bootstrap_cluster
  File "build/bdist.linux-x86_64/egg/bcbiovm/aws/bootstrap.py", line 46, in bootstrap
  File "build/bdist.linux-x86_64/egg/bcbiovm/aws/bootstrap.py", line 60, in _bootstrap_baseline
  File "build/bdist.linux-x86_64/egg/bcbiovm/aws/common.py", line 122, in run_ansible_pb
NameError: global name 'ansible_utils' is not defined

This prevents the cluster from starting.

Likely cause Line 122 of bcbiovm/aws/common.py reads:

if ansible.utils:
    ansible_utils.VERBOSITY = args.verbose - 1

I suspect this is a typo for ansible.utils.VERBOSITY. I commented lines 121-122 out and re-built my local copy of the egg, at which point my cluster was able to build completely.

chapmanb commented 7 years ago

David; Thanks so much for the heads up and sorry about the typo. This is fixed in the development version and I'll push a new conda package as well. Thanks again.