diff --git a/Jenkinsfile b/Jenkinsfile index 5ea3d08..a971e03 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -21,6 +21,7 @@ pipeline { } stage("conda") { steps { + sh 'conda config --add channels bioconda' sh 'conda env update -n base --file environment.yml' } } @@ -36,18 +37,14 @@ pipeline { } stage("lint") { steps { - container(miniforge3) { - dir('auto-updated-bioconda-recipes') { - sh 'conda -n install python=3.10 bioconda-utils' - sh 'bioconda-utils lint recipes/ --packages autobigs-cli' - } + dir('auto-updated-bioconda-recipes') { + sh 'bioconda-utils lint recipes/ --packages autobigs-cli' } } } stage("build") { steps { dir('auto-updated-bioconda-recipes') { - sh 'conda install autobigs-engine=$(python ../pypi_latest_ver.py autoBIGS.engine)' sh 'conda build recipes/autobigs-cli' } } diff --git a/auto-updated-bioconda-recipes b/auto-updated-bioconda-recipes new file mode 160000 index 0000000..5b96026 --- /dev/null +++ b/auto-updated-bioconda-recipes @@ -0,0 +1 @@ +Subproject commit 5b96026a21dcf8aaeb86115c2422633b099856c4 diff --git a/environment.yml b/environment.yml index 5cbd326..b3ee1b4 100644 --- a/environment.yml +++ b/environment.yml @@ -6,3 +6,5 @@ dependencies: - conda-build - grayskull - git + - bioconda-utils + - python=3.10.* \ No newline at end of file