CPSR is distributed alongside the Personal Cancer Genome Reporter (PCGR), so please follow the PCGR installation steps to install CPSR, either through Docker, Apptainer/Singularity, or Conda.
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.