ydeng/autoBIGS.cli-bioconda
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Added step to add bioconda as channel for dependencies
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Harrison Deng 2025-02-19 19:15:58 +00:00
parent 1def4bb15f
commit bb04a02af3
3 changed files with 6 additions and 6 deletions
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9
Jenkinsfile vendored
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@ -21,6 +21,7 @@ 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'
} }
} }
@ -36,18 +37,14 @@ pipeline {
} }
stage("lint") { stage("lint") {
steps { steps {
container(miniforge3) { dir('auto-updated-bioconda-recipes') {
dir('auto-updated-bioconda-recipes') { sh 'bioconda-utils lint recipes/ --packages autobigs-cli'
sh 'conda -n install python=3.10 bioconda-utils'
sh 'bioconda-utils lint recipes/ --packages autobigs-cli'
}
} }
} }
} }
stage("build") { stage("build") {
steps { steps {
dir('auto-updated-bioconda-recipes') { dir('auto-updated-bioconda-recipes') {
sh 'conda install autobigs-engine=$(python ../pypi_latest_ver.py autoBIGS.engine)'
sh 'conda build recipes/autobigs-cli' sh 'conda build recipes/autobigs-cli'
} }
} }

1
auto-updated-bioconda-recipes Submodule

@ -0,0 +1 @@
Subproject commit 5b96026a21dcf8aaeb86115c2422633b099856c4

2
environment.yml
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@ -6,3 +6,5 @@ dependencies:
- conda-build - conda-build
- grayskull - grayskull
- git - git
- bioconda-utils
- python=3.10.*