ydeng/autoBIGS.engine-bioconda
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changed to using submodule
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Harrison Deng 2025-02-26 14:32:02 +00:00
parent 453c25e758
commit 41441c6aae
4 changed files with 18 additions and 33 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

44
Jenkinsfile vendored
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@ -11,7 +11,6 @@ pipeline {
parallel {
stage("recipes repo") {
steps {
sh 'git clone https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git'
dir('auto-updated-bioconda-recipes') {
sh 'git checkout update-autobigs-engine'
}
@ -33,46 +32,27 @@ pipeline {
}
stage("build") {
steps {
dir('auto-updated-bioconda-recipes') {
sh 'conda build recipes/autobigs-engine --output-folder ./conda-bld'
}
sh 'conda build auto-updated-bioconda-recipes/recipes/autobigs-engine --output-folder ./conda-bld'
}
}
stage('publish') {
parallel {
stage("archive") {
stage("publish to bioconda") {
stages {
stage('lint') {
steps {
archiveArtifacts artifacts: './conda-bld/**/*.conda', followSymlinks: false
}
}
stage("bioconda") {
stages {
stage('lint') {
steps {
dir('auto-updated-bioconda-recipes') {
sh 'bioconda-utils lint recipes/ --packages autobigs-engine'
}
}
}
stage('commit') {
environment {
TOKEN = credentials('github.com')
}
steps {
dir('auto-updated-bioconda-recipes') {
sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to $(python ../pypi_latest_ver.py autoBIGS.engine)."'
sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-engine'
}
}
dir('auto-updated-bioconda-recipes') {
sh 'bioconda-utils lint recipes/ --packages autobigs-engine'
}
}
}
stage('git.reslate.systems') {
stage('commit') {
environment {
AUTH = credentials('git.reslate.systems')
TOKEN = credentials('github.com')
}
steps {
sh 'curl --user AUTH_USR:AUTH_PSW --upload-file ./conda-bld/**/*.conda https://git.reslate.systems/api/packages/${AUTH_USR}/conda/package-1.0.conda'
dir('auto-updated-bioconda-recipes') {
sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to $(python ../pypi_latest_ver.py autoBIGS.engine)."'
sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-engine'
}
}
}
}

1
auto-updated-bioconda-recipes Submodule

@ -0,0 +1 @@
Subproject commit 8bdf7d8e65ec383ff3de875814a0b67abeba6ad7

3
environment.yml
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@ -8,4 +8,5 @@ dependencies:
- git
- bioconda-utils
- python=3.10.*
- curl
- curl
- conda-verify