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Astrocyte
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BioHPC
astrocyte_example_wordcount
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c5b25d04
Commit
c5b25d04
authored
4 years ago
by
Hololens Test
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Test extension of gitlab
parent
facd08aa
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1 merge request
!3
Merge new CI pipeline with the changes from Peng.
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.gitlab-ci.yml
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c5b25d04
# Run our tests against a specific version of astrocyte
before_script
:
-
module load astrocyte/0.4.0
stages
:
-
check
-
test
-
test_docker
-
cache_docker
-
test_singularity
-
cache_singularity
# Execute this script for everybody. YAML anchor.
.all-script-before
:
&all-script-before
-
pwd
-
env
-
ls -laht
-
whoami
### All base jobs.
# Astrocyte jobs, assumed to need to run on the cluster where they have access to the module lists.
.astrocyte
:
before_script
:
-
*all-script-before
-
module load astrocyte/0.4.0
tags
:
-
cluster_node
.docker
:
before_script
:
-
*all-script-before
-
docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
### Setup scripts
before_script
:
-
*all-script-before
# This performs validation of the astrocyte_pkg.yml file
astrocyte_check
:
extends
:
.astrocyte
stage
:
check
script
:
-
astrocyte_cli check "$CI_PROJECT_DIR"
# This runs the workflow with test data and does a simple
# check for the expected output file
astrocyte_test
:
extends
:
.astrocyte
stage
:
test
script
:
-
astrocyte_cli test "$CI_PROJECT_DIR"
-
test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
# This runs the workflow, opting to use Docker containers.
docker_astrocyte_test
:
stage
:
test_docker
script
:
-
echo "Run astrocyte using dockerhub/docker.io registry pulls"
cache_docker_image
:
stage
:
cache_docker
script
:
-
echo "Pull Docker image from the docker.io registry, re-tag, and push to our GitLab"
singularity_astrocyte_test
:
stage
:
test_singularity
script
:
-
echo "Run astrocyte using singularity registry pulls"
cache_singularity_image
:
stage
:
cache_singularity
script
:
-
echo "Pull from our gitlab OCI registry using singularity and save as SIF on the cluster"
# This verifies we can install the shiny vizapp dependencies
# and start the vizapp running.
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