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Jenkinsfile
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def isPullRequest = false
pipeline {
agent any
stages {
stage('First stage') {
steps {
script {
isPullRequest = env.CHANGE_ID != null
}
sh 'printenv'
}
}
stage('Build - dependent software container') {
when {
anyOf {
expression { isPullRequest == false && env.BRANCH_NAME == 'master' }
expression { isPullRequest == false && env.BRANCH_NAME == 'develop' }
}
}
environment {
DOCKERHUB_CREDS = credentials('dokcerhhub')
DOCKER_REGISTRY_URL = credentials('dockerhub_registry_url')
CGU_CREDS = credentials('cgu-registry')
CGU_REGISTRY_URL = credentials('cgu_registry_url')
REPOSITORY = credentials('REPOSITORY')
}
steps{
sh '''
for versionFilePath in $( git --no-pager diff --name-only @~..@ | grep VERSION);
do
folder=${versionFilePath%"/VERSION"};
IMAGE_NAME=${folder##*/};
tmpName="image-$RANDOM";
docker build $folder --file $folder/Dockerfile --tag $tmpName --no-cache;
VERSION=${BRANCH_NAME};
echo "${DOCKERHUB_CREDS_PSW}" | docker login ${DOCKER_REGISTRY_URL} -u ${DOCKERHUB_CREDS_USR} --password-stdin;
IMAGE_ID=${DOCKER_REGISTRY_URL}/${REPOSITORY}/$IMAGE_NAME;
docker tag $tmpName $IMAGE_ID:$VERSION;
docker push $IMAGE_ID:$VERSION;
docker logout;
echo "${CGU_CREDS_PSW}" | docker login ${CGU_REGISTRY_URL} -u ${CGU_CREDS_USR} --password-stdin
IMAGE_ID="docker-registry.cgu10.igp.uu.se/gmsuppsala/$IMAGE_NAME";
docker tag $tmpName $IMAGE_ID:$VERSION;
docker push $IMAGE_ID:$VERSION;
docker logout;
done;
'''
}
}
stage('Build - test container') {
when {
anyOf {
expression { isPullRequest == false && env.BRANCH_NAME == 'master' }
expression { isPullRequest == false && env.BRANCH_NAME == 'develop' }
}
}
environment {
CGU_CREDS = credentials('cgu-registry')
CGU_REGISTRY_URL = credentials('cgu_registry_url')
REPOSITORY = credentials('REPOSITORY')
}
steps{
sh '''
tmpName1="image1-$RANDOM";
docker build . --file tests/dockerfiles/test_env.dockerfile --tag $tmpName1 --no-cache;
VERSION=${BRANCH_NAME};
IMAGE_NAME1="test_env_somatic"
echo "${CGU_CREDS_PSW}" | docker login ${CGU_REGISTRY_URL} -u ${CGU_CREDS_USR} --password-stdin;
IMAGE_ID1="docker-registry.cgu10.igp.uu.se/gmsuppsala/$IMAGE_NAME1";
docker tag $tmpName1 $IMAGE_ID1:$VERSION;
docker push $IMAGE_ID1:$VERSION;
tmpName2="image2-$RANDOM";
docker build . --file tests/dockerfiles/test_env_full.dockerfile --tag $tmpName2 --no-cache;
VERSION=${BRANCH_NAME};
IMAGE_NAME2="test_env_somatic_full"
echo "${CGU_CREDS_PSW}" | docker login ${CGU_REGISTRY_URL} -u ${CGU_CREDS_USR} --password-stdin;
IMAGE_ID2="docker-registry.cgu10.igp.uu.se/gmsuppsala/$IMAGE_NAME2";
docker tag $tmpName2 $IMAGE_ID2:$VERSION;
docker push $IMAGE_ID2:$VERSION;
docker logout;
'''
}
}
stage('Dry run tests') {
when {
expression { isPullRequest == true }
}
agent {
dockerfile {
filename 'tests/dockerfiles/twist_dna_working.dockerfile'
dir './'
args '-u 0 --privileged -v $HOME/.m2:/home/jenkins/.m2:ro -v /beegfs-storage:/beegfs-storage:ro'
registryUrl 'https://docker-registry.cgu10.igp.uu.se'
registryCredentialsId 'cgu-registry'
}
}
steps {
sh 'cp -r /data_twist_dna_fgbio . && snakemake -n -s /Twist_DNA/Twist_DNA.smk --directory /data_twist_dna_fgbio'
sh 'cp -r /data_twist_dna_markdup . && snakemake -n -s Twist_DNA.smk --directory /data_twist_dna_markdup'
sh 'cp -r /data_twist_dna_gpu . && snakemake -n -s Twist_DNA.smk --directory /data_twist_dna_gpu'
sh 'cp -r /data_twist_dna_cutadapt . && snakemake -n -s Twist_DNA.smk --directory /data_twist_dna_cutadapt'
sh 'cp -r /data_twist_dna_fastp . && snakemake -n -s Twist_DNA.smk --directory /data_twist_dna_fastp'
sh 'cp -r /data_demultiplex . && snakemake -n -s demultiplex.smk --directory /data_demultiplex/'
}
}
stage('Small dataset 1') {
when {
anyOf {
expression { env.BRANCH_NAME == 'master' || isPullRequest == true }
expression { env.BRANCH_NAME == 'develop' || isPullRequest == true }
}
}
agent {
dockerfile {
filename 'tests/dockerfiles/twist_dna_working_full.dockerfile'
dir './'
args '-u 0 --privileged -v $HOME/.m2:/home/jenkins/.m2:ro -v /beegfs-storage:/beegfs-storage:ro'
registryUrl 'https://docker-registry.cgu10.igp.uu.se'
registryCredentialsId 'cgu-registry'
}
}
steps {
sh 'snakemake -j 4 -s /Twist_DNA/Twist_DNA.smk --directory /data_twist_dna_markdup --use-singularity --singularity-prefix /Twist_DNA --singularity-args " --cleanenv --bind /beegfs-storage --bind /projects --bind /data --bind /Twist_DNA "'
}
}
stage('Small dataset 2') {
when {
anyOf {
expression { env.BRANCH_NAME == 'master' && isPullRequest == false }
expression { env.BRANCH_NAME == 'develop' && isPullRequest == false }
}
}
agent {
dockerfile {
filename 'tests/dockerfiles/twist_dna_working_full.dockerfile'
dir './'
args '-u 0 --privileged -v $HOME/.m2:/home/jenkins/.m2:ro -v /beegfs-storage:/beegfs-storage:ro'
registryUrl 'https://docker-registry.cgu10.igp.uu.se'
registryCredentialsId 'cgu-registry'
}
}
steps {
sh 'snakemake -j 4 -s /Twist_DNA/Twist_DNA.smk --directory /data_twist_dna_fgbio --use-singularity --singularity-prefix /Twist_DNA --singularity-args " --cleanenv --bind /beegfs-storage --bind /projects --bind /data --bind /Twist_DNA "'
sh 'snakemake -j 4 -s /Twist_DNA/Twist_DNA.smk --directory /data_twist_dna_cutadapt --use-singularity --singularity-prefix /Twist_DNA --singularity-args " --cleanenv --bind /beegfs-storage --bind /projects --bind /data --bind /Twist_DNA "'
sh 'snakemake -j 4 -s /Twist_DNA/Twist_DNA.smk --directory /data_twist_dna_fastp --use-singularity --singularity-prefix /Twist_DNA --singularity-args " --cleanenv --bind /beegfs-storage --bind /projects --bind /data --bind /Twist_DNA "'
}
}
}
post {
always {
sh 'docker image prune -fa'
}
}
}