Harrison Deng
0e5c323070
Some checks failed
autoBIGS.galaxy/pipeline/head There was a failure building this commit
33 lines
1.1 KiB
Groovy
33 lines
1.1 KiB
Groovy
pipeline {
|
|
agent {
|
|
kubernetes {
|
|
cloud 'rsys-devel'
|
|
defaultContainer 'miniforge3'
|
|
inheritFrom 'miniforge'
|
|
}
|
|
}
|
|
|
|
stages {
|
|
stage ("install") {
|
|
steps {
|
|
sh 'conda install python==3.12.7 pip -y -q'
|
|
sh 'useradd galaxy -m'
|
|
sh 'apt-get update'
|
|
sh 'apt-get install sudo -y'
|
|
sh 'pip install -r requirements.txt'
|
|
}
|
|
}
|
|
stage ("lint") {
|
|
steps {
|
|
sh "sudo -u galaxy planemo lint autobigs-cli.xml"
|
|
}
|
|
}
|
|
stage ("test") {
|
|
steps {
|
|
sh 'sudo -u galaxy mkdir test_results'
|
|
sh "sudo -u galaxy planemo test autobigs-cli.xml --test_output_junit test_results/junit_results.xml --test_output_json test_results/results.json --test_output test_results/human.html"
|
|
xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results/junit_report.xml', stopProcessingIfError: true)]
|
|
}
|
|
}
|
|
}
|
|
} |