ydeng/autoBIGS.cli-bioconda
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Updated pipeline to use submodule of recipe repo fork
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Harrison Deng 2025-02-26 17:22:14 +00:00
parent 65a3bc3f64
commit c0a5c34380
3 changed files with 35 additions and 21 deletions
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3
.gitmodules vendored Normal file
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@ -0,0 +1,3 @@
[submodule "auto-updated-bioconda-recipes"]
path = auto-updated-bioconda-recipes
url = https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git

52
Jenkinsfile vendored
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@ -6,14 +6,23 @@ pipeline {
inheritFrom 'miniforge'
}
}
environment {
TOOL_VER = """${sh(
returnStdout: true,
script: 'python pypi_latest_ver.py autoBIGS.cli'
)}"""
}
stages {
stage("prepare") {
parallel {
stage("recipes repo") {
steps {
sh 'git clone https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git'
sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.cli-bioconda_main'
sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.cli-bioconda_main/auto-updated-bioconda-recipes'
sh 'git submodule init'
sh 'git submodule update'
dir('auto-updated-bioconda-recipes') {
sh 'git checkout update-autobigs-cli'
sh 'git checkout -b update-autobigs-cli-${TOOL_VER}'
}
}
}
@ -30,31 +39,32 @@ pipeline {
sh 'grayskull pypi autoBIGS.cli --maintainers "Harrison Deng"'
sh 'python patch_recipe.py'
sh 'cp -r autobigs-cli/* auto-updated-bioconda-recipes/recipes/autobigs-cli/.'
sh 'cat auto-updated-bioconda-recipes/recipes/autobigs-cli/meta.yaml'
}
}
stage("lint") {
steps {
dir('auto-updated-bioconda-recipes') {
sh 'bioconda-utils lint recipes/ --packages autobigs-cli'
}
}
}
stage("build") {
steps {
dir('auto-updated-bioconda-recipes') {
sh 'conda build recipes/autobigs-cli'
}
sh 'conda build auto-updated-bioconda-recipes/recipes/autobigs-cli --output-folder ./conda-bld'
}
}
stage("commit") {
environment {
TOKEN = credentials('github.com')
}
steps {
dir('auto-updated-bioconda-recipes') {
sh 'git commit -a -m "Automatically updated autobigs-cli bioconda recipe to $(python ../pypi_latest_ver.py autoBIGS.cli)."'
sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-cli'
stage("publish to bioconda") {
stages {
stage('lint') {
steps {
dir('auto-updated-bioconda-recipes') {
sh 'bioconda-utils lint recipes/ --packages autobigs-cli'
}
}
}
stage('commit') {
environment {
TOKEN = credentials('github.com')
}
steps {
dir('auto-updated-bioconda-recipes') {
sh 'git commit -a -m "Automatically updated autobigs-cli bioconda recipe to ${TOOL_VER}."'
sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-cli'
}
}
}
}
}

1
auto-updated-bioconda-recipes Submodule

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Subproject commit d3a720566fbbc63e32571ade8d643a6f6b1a4e25