Commit 4b4cc7a7 authored by Devin OKelly's avatar Devin OKelly
Browse files

Switchable configs for astrocyte_pkg.yml runs of astrocyte.

parent 50489b22
......@@ -18,7 +18,6 @@ variables:
- whoami
### All base jobs.
# Astrocyte jobs, assumed to need to run on the cluster where they have access to the module lists.
......@@ -82,22 +81,32 @@ astrocyte_test:
artifacts:
paths:
- $CI_PROJECT_DIR/workflow/.nextflow.log
# This runs the workflow, opting to use Docker containers.
docker_astrocyte_test:
stage: test_docker
script:
- docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
# Note the biohpc_docker.config replacement.
- sed -i 's|nextflow_config: \x27biohpc.config\x27|nextflow_config: \x27biohpc_docker.config\x27|' astrocyte_pkg.yml
- echo "Run astrocyte using dockerhub/docker.io registry pulls"
- astrocyte_cli run "$CI_PROJECT_DIR" --option=bg
- test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
cache_docker_image:
stage: cache_docker
script:
- docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
- echo "Pull Docker image from the docker.io registry, re-tag, and push to our GitLab"
- echo "Need to know what the docker image is ahead of time"
singularity_astrocyte_test:
stage: test_singularity
script:
- echo "Run astrocyte using singularity registry pulls"
# Note the biohpc_singularity.config replacement.
- sed -i 's|nextflow_config: \x27biohpc.config\x27|nextflow_config: \x27biohpc_singularity.config\x27|' astrocyte_pkg.yml
- echo "Run astrocyte using singularity with dockerhub/docker.io registry pulls"
- astrocyte_cli run "$CI_PROJECT_DIR" --option=bg
- test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
cache_singularity_image:
stage: cache_singularity
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment