ydeng/autoBIGS.engine-bioconda
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Removed submodule
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Harrison Deng 2025-02-26 18:08:18 +00:00
parent 4c59c4a5b1
commit 9cf6a699c6
3 changed files with 16 additions and 24 deletions
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3
.gitmodules vendored
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@ -1,3 +0,0 @@
[submodule "auto-updated-bioconda-recipes"]
path = auto-updated-bioconda-recipes
url = https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git

36
Jenkinsfile vendored
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@ -19,8 +19,7 @@ pipeline {
steps { steps {
sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.engine-bioconda_main' sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.engine-bioconda_main'
sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.engine-bioconda_main/auto-updated-bioconda-recipes' sh 'git config --global --add safe.directory /home/jenkins/agent/workspace/autoBIGS.engine-bioconda_main/auto-updated-bioconda-recipes'
sh 'git submodule init' sh 'git clone https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git'
sh 'git submodule update'
dir('auto-updated-bioconda-recipes') { dir('auto-updated-bioconda-recipes') {
sh 'git checkout -b update-autobigs-engine-${TOOL_VER}' sh 'git checkout -b update-autobigs-engine-${TOOL_VER}'
} }
@ -28,6 +27,7 @@ pipeline {
} }
stage("conda") { stage("conda") {
steps { steps {
sh 'conda config --add channels bioconda'
sh 'conda env update -n base --file environment.yml' sh 'conda env update -n base --file environment.yml'
} }
} }
@ -45,25 +45,21 @@ pipeline {
sh 'conda build auto-updated-bioconda-recipes/recipes/autobigs-engine --output-folder ./conda-bld' sh 'conda build auto-updated-bioconda-recipes/recipes/autobigs-engine --output-folder ./conda-bld'
} }
} }
stage("publish to bioconda") { stage('lint') {
stages { steps {
stage('lint') { dir('auto-updated-bioconda-recipes') {
steps { sh 'bioconda-utils lint recipes/ --packages autobigs-engine'
dir('auto-updated-bioconda-recipes') {
sh 'bioconda-utils lint recipes/ --packages autobigs-engine'
}
}
} }
stage('commit') { }
environment { }
TOKEN = credentials('github.com') stage('commit') {
} environment {
steps { TOKEN = credentials('github.com')
dir('auto-updated-bioconda-recipes') { }
sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to ${TOOL_VER}."' steps {
sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-engine' dir('auto-updated-bioconda-recipes') {
} sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to ${TOOL_VER}."'
} sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-engine-${TOOL_VER}'
} }
} }
} }

1
auto-updated-bioconda-recipes

@ -1 +0,0 @@
Subproject commit 0dee939d053ccc2d347ef45563a3b45bf6ad1e84