A pipeline to compute the CN, SNV, ... on TWIST sequences from the CCLF program
-
git clone https://github.com/broadinstitute/CCLF_TWIST -
(Recommended in a conda or virtual environment)
conda create -n cclf python=3.6 -
Run
cd CCLF_TWIST && pip install -r requirements.txtto load all the dependencies -
information on the pipeline running on Terra is given here
-
you also have to get the JKBio package by running (from within the same parent folder as where CCLF_TWIST is):
cd .. && git clone https://github.com/jkobject/JKBIO -
you might also have to load the dependencies here:
cd JKBio && pip install -r requirements.txt
@BroadInstitute
Jérémie Kalfon @jkobject Gwen Miller Aniket Shetty