CPSR is distributed alongside the Personal Cancer Genome Reporter (PCGR), so please follow the PCGR installation steps to install CPSR.
We recommend conda as the simplest framework to install PCGR and CPSR, using either a MacOS or a Linux platform.
Assuming you have installed the pcgr and
pcgrr conda envs as described in the above links at
e.g. /home/user/projects/cpsr_proj1/conda/env/, you can
load the pcgr environment and check that CPSR is installed
with the following:
(base) $ cd /home/user/projects/cpsr_proj1
(base) $ conda activate ./conda/env/pcgr
(/home/user/projects/cpsr_proj1/conda/env/pcgr) $ which cpsr
/home/user/projects/cpsr_proj1/conda/env/pcgr/bin/cpsr
(/home/user/projects/cpsr_proj1/conda/env/pcgr/bin/cpsr) $ cpsr -h
[...]You should now be all set up to run CPSR! Continue on to an example run.