Problem installing quiver

Question

[biomagician]

Hi,

I have a problem with the Quiver installation.

I did this:

git clone https://github.com/PacificBiosciences/ConsensusCore output/software/ConsensusCore/
cd output/software/ConsensusCore
source activate python2env # i tried python2 setup.py install and python3 setup.py install but they failed quickly
python setup.py install
brew install swig # needed for ConsensusCore

i am in python2env
git clone https://github.com/PacificBiosciences/pbcore output/software/pbcore/
cd output/software/pbcore
pip install -r requirements.txt
python setup.py install

git clone https://github.com/PacificBiosciences/GenomicConsensus/ output/software/GenomicConsensus/
cd output/software/GenomicConsensus
python setup.py install (while in python2env)

Then, if I try the command 'quiver --help', I get this:

quiver --help
Traceback (most recent call last):
  File "/Users/cr517/anaconda/envs/python2env/bin/variantCaller", line 4, in <module>
    __import__('pkg_resources').run_script('GenomicConsensus==2.2.0', 'variantCaller')
  File "/Users/cr517/anaconda/envs/python2env/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 744, in run_script
  File "/Users/cr517/anaconda/envs/python2env/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 1499, in run_script
  File "/Users/cr517/anaconda/envs/python2env/lib/python2.7/site-packages/GenomicConsensus-2.2.0-py2.7.egg/EGG-INFO/scripts/variantCaller", line 5, in <module>
    sys.exit(main())
  File "/Users/cr517/anaconda/envs/python2env/lib/python2.7/site-packages/GenomicConsensus-2.2.0-py2.7.egg/GenomicConsensus/main.py", line 419, in main
    parser=get_parser(),
  File "/Users/cr517/anaconda/envs/python2env/lib/python2.7/site-packages/GenomicConsensus-2.2.0-py2.7.egg/GenomicConsensus/options.py", line 130, in get_parser
    tcp.add_choice_str(
AttributeError: 'ToolContractParser' object has no attribute 'add_choice_str'

Can somebody help me, please?

Best wishes,

C.

Answer 1

[johnj]

To anyone still having this problem:

"ToolContractParser" is part of "pbcommand". If you use "pip" to install it, you will likely get version 0.3.x. By going to the github site for pbcomand:

https://github.com/PacificBiosciences/pbcommand/releases

and downloading and installing version 0.2.12, I was able to resolve this problem. So it appears the newest version of GenomicConsensus does NOT work properly with the newest version of pbcommand.

[emily.ebel]

Installing the old version 0.2.12 did not work for me, but installing the newest version 0.6.X did. That is, download the 'master' version from https://github.com/PacificBiosciences/pbcommand, unzip, cd, and type 'make'.