CCRR: Complex Chromosomal Rearrangements Resolver

1. Installation

1. Uncompress ccrr1.2.zip

   unzip ccrr1.2.zip

2. Prepare

   python install.py -sequenza -manta -delly -svaba -gridss \
                       -lumpy -soreca -purple -sclust -cnvkit \
                       -ref 'hg19&hg38'

   This script will automatically download the dependency data for the tools you selected and build the Dockerfile.

3. Obtain licenses for Mosek and Gurobi
   • Gurobi: Apply for a WLS Compute Server license and store it in the same directory as the Dockerfile, named gurobi.lic. For more information, visit www.gurobi.com
   • Mosek: Obtain a Mosek license and store it in the same directory as the Dockerfile, named mosek.lic. For more information, visit www.mosek.com
4. Build Docker image

   docker build --pull --rm --build-arg GITHUB_PAT=[GITHUB_PAT] -f dockerfile -t ccrr:v1 .

5. Run a container

   docker run -v $(pwd)/share:/home/2.share -v $(pwd)/wd:/home/3.wd -d -it --name ccrr ccrr:v1

   docker exec -it ccrr /bin/bash 

2. Testing

ccrr -mode test

3. Quick Start

nohup ccrr -mode default -prefix task_id\
        -normal [normal.bam] --normal-id [normal-id] \
        -tumor [tumor.bam] --tumor-id [tumor-id] \
        --genome-version hg19 -reference [hg19.fa] \
        -threads 30 -g 200 >log 2>&1 &