Question: Problem installing quiver
0
gravatar for cristian
20 months ago by
cristian180
cristian180 wrote:

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.

arrow pacbio polishing quiver • 1.2k views
ADD COMMENTlink modified 16 months ago by johnj0 • written 20 months ago by cristian180
0
gravatar for johnj
16 months ago by
johnj0
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:

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.

ADD COMMENTlink modified 16 months ago • written 16 months 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 https://github.com/PacificBiosciences/pbcommand, unzip, cd, and type 'make'.

ADD REPLYlink written 15 months ago by emily.ebel0
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