Commit d6880eee authored by van den Berg's avatar van den Berg
Browse files

Use environment conda to run integration

parent 2a54274e
Pipeline #3619 canceled with stages
in 7 minutes and 12 seconds
...@@ -9,11 +9,11 @@ variables: ...@@ -9,11 +9,11 @@ variables:
.singularity_before_script_anchor: &singularity_before_script_anchor .singularity_before_script_anchor: &singularity_before_script_anchor
before_script: before_script:
- pip install -r requirements.txt
- pip install -r requirements-dev.txt
- export BASETEMP=$RUN_BASE_DIR/$CI_COMMIT_REF_NAME/$CI_JOB_ID - export BASETEMP=$RUN_BASE_DIR/$CI_COMMIT_REF_NAME/$CI_JOB_ID
- source ${CONDA_SH}
- conda activate hutspot-pipeline
- export PATH=${PATH}:${SINGULARITY_PATH}
- echo $BASETEMP - echo $BASETEMP
- mkdir -p $BASETEMP
stages: stages:
- sanity - sanity
...@@ -42,7 +42,7 @@ test_dry_run: ...@@ -42,7 +42,7 @@ test_dry_run:
test_integration: test_integration:
<<: *singularity_before_script_anchor <<: *singularity_before_script_anchor
script: script:
- pytest-3 --tag integration --basetemp ${BASETEMP} --keep-workflow-wd - pytest --tag integration --basetemp ${BASETEMP} --keep-workflow-wd
tags: tags:
- slurm - slurm
stage: integration stage: integration
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