Requirements:

$ docker -v
Docker version 17.03.0-ce, build 60ccb22
$ wget

Step 1: Prepare build environment

git clone https://github.com/mctp/crisp-build
cp <<NOVOALIGN LICENSE KEY>> crisp-build/novoalign.lic
cd crisp-build

Step 2: Build GXCORE Docker image This step provides

# pre-build base image recommended (~10min)
bash docker/pull_image_gxcore.sh
# alternatively build from scratch (~2-3h)
bash docker/build_image_gxcore.sh

Step 3: Build GXUSER Docker image This step add user credentials to the docker image

bash docker/build_image_gxuser.sh

Step 4: Prepare dependencies

bash deps-build.sh

Step 5: Build CRISP and CODAC Docker images

bash docker/build_image_crisp.sh
bash docker/build_image_codac.sh

Step 6: Test CRISP image:

wget -P repo https://storage.googleapis.com/crisp-mctp/test.data/fastq/mctp_SI_12764_C8LJ1ANXX_6_1.fq.gz
wget -P repo https://storage.googleapis.com/crisp-mctp/test.data/fastq/mctp_SI_12764_C8LJ1ANXX_6_2.fq.gz
bash test/crisp-run/init.sh

Step 7: Test CODAC image:

wget -P repo https://storage.googleapis.com/crisp-mctp/test.data/crisp/2.0.0/VCaP-poly-SI_12764-C8LJ1ANXX.tar.gz
tar xf repo/VCaP-poly-SI_12764-C8LJ1ANXX.tar.gz -C repo
bash test/codac-run/init.sh