Question: Problem installing quiver
gravatar for cristian
3.3 years ago by
cristian240 wrote:


I have a problem with the Quiver installation.

I did this:

git clone output/software/ConsensusCore/
cd output/software/ConsensusCore
source activate python2env # i tried python2 install and python3 install but they failed quickly
python install
brew install swig # needed for ConsensusCore

i am in python2env
git clone output/software/pbcore/
cd output/software/pbcore
pip install -r requirements.txt
python install

git clone output/software/GenomicConsensus/
cd output/software/GenomicConsensus
python 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/", 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/", 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>
  File "/Users/cr517/anaconda/envs/python2env/lib/python2.7/site-packages/GenomicConsensus-2.2.0-py2.7.egg/GenomicConsensus/", line 419, in main
  File "/Users/cr517/anaconda/envs/python2env/lib/python2.7/site-packages/GenomicConsensus-2.2.0-py2.7.egg/GenomicConsensus/", line 130, in get_parser
AttributeError: 'ToolContractParser' object has no attribute 'add_choice_str'

Can somebody help me, please?

Best wishes,


arrow pacbio polishing quiver • 1.8k views
ADD COMMENTlink modified 3.1 years ago by johnj0 • written 3.3 years ago by cristian240
gravatar for johnj
3.1 years ago by
United States
johnj0 wrote:

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:

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.

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by johnj0

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, unzip, cd, and type 'make'.

ADD REPLYlink written 2.9 years ago by emily.ebel0
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