65 lines
2.5 KiB
Groovy
65 lines
2.5 KiB
Groovy
pipeline {
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agent {
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kubernetes {
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cloud 'rsys-devel'
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defaultContainer 'miniforge3'
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inheritFrom 'miniforge'
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}
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}
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stages {
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stage("prepare") {
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parallel {
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stage("recipes repo") {
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steps {
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sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.engine-bioconda_main'
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sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.engine-bioconda_main/auto-updated-bioconda-recipes'
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sh 'git submodule init'
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sh 'git submodule update'
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dir('auto-updated-bioconda-recipes') {
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sh 'git checkout update-autobigs-engine'
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}
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}
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}
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stage("conda") {
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steps {
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sh 'conda env update -n base --file environment.yml'
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}
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}
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}
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}
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stage("generate recipe") {
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steps {
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sh 'grayskull pypi autoBIGS.engine --maintainers "Harrison Deng"'
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sh 'python patch_recipe.py'
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sh 'cp -r autobigs-engine/* auto-updated-bioconda-recipes/recipes/autobigs-engine/.'
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}
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}
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stage("build") {
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steps {
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sh 'conda build auto-updated-bioconda-recipes/recipes/autobigs-engine --output-folder ./conda-bld'
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}
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}
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stage("publish to bioconda") {
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stages {
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stage('lint') {
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steps {
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dir('auto-updated-bioconda-recipes') {
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sh 'bioconda-utils lint recipes/ --packages autobigs-engine'
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}
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}
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}
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stage('commit') {
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environment {
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TOKEN = credentials('github.com')
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}
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steps {
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dir('auto-updated-bioconda-recipes') {
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sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to $(python ../pypi_latest_ver.py autoBIGS.engine)."'
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sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-engine'
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}
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}
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}
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}
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}
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}
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} |