Commit 5c395116 authored by van den Berg's avatar van den Berg
Browse files

Add singularity anchor

parent dfb090d0
Pipeline #3614 failed with stages
in 2 minutes and 42 seconds
......@@ -7,6 +7,15 @@ variables:
- pip3 install -r requirements.txt
- pip3 install -r requirements-dev.txt
.singularity_before_script_anchor: &singularity_before_script_anchor
before_script:
- apt update -y && apt install python3-pip -y
- pip3 install -r requirements.txt
- pip3 install -r requirements-dev.txt
- export BASETEMP=$RUN_BASE_DIR/$CI_COMMIT_REF_NAME/$CI_JOB_ID
- echo $BASETEMP
- mkdir -p $BASETEMP
stages:
- sanity
- dry-run
......@@ -32,9 +41,7 @@ test_dry_run:
test_integration:
<<: *docker_before_script_anchor
before_script:
- export BASETEMP=$RUN_BASE_DIR/$CI_COMMIT_REF_NAME/$CI_JOB_ID
<<: *singularity_before_script_anchor
script:
- pytest-3 --tag integration --basetemp ${BASETEMP} --keep-workflow-wd
image: lumc/singularity-snakemake:3.5.2-5.9.1
......
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