autoBIGS.engine-bioconda/Jenkinsfile

pipeline {
    agent {
        kubernetes {
            cloud 'rsys-devel'
            defaultContainer 'miniforge3'
            inheritFrom 'miniforge'
        }
    }
    stages {
        stage("prepare") {
            parallel {
                stage("recipes repo") {
                    steps {
                        sh 'git clone https://github.com/Syph-and-VPD-Lab/bioconda-recipes.git'
                        dir('bioconda-recipes') {
                            sh 'git pull'
                            sh 'git pull origin update-autobigs-engine'
                        }
                    }
                }
                stage("conda") {
                    steps {
                        sh 'conda env update -n base --file environment.yml'
                    }
                }
            }
        }
        stage("generate recipe") {
            steps {
                sh 'grayskull pypi autobigs.engine --maintainers "Harrison Deng"'
                sh 'python scripts/adapt_names.py autobigs.engine'
            }
        }
        stage("build") {
            steps {
                sh 'conda build autobigs-engine'
            }
        }
        stage("commit") {
            environment {
                TOKEN = credentials('github.com')
            }
            steps {
                dir('bioconda-recipes') {
                    sh 'cp -r ../autobigs-engine/* recipes/autobigs-engine/.'
                    sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to $(python ../scripts/package_latest_version.py autoBIGS.engine)."'
                    sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/bioconda-recipes.git update-autobigs-engine'
                }
            }
        }
    }
}