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Commit 9af5bb5a authored by Hololens Test's avatar Hololens Test
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Merge branch 'LocalDockerRegistry' of...

Merge branch 'LocalDockerRegistry' of git.biohpc.swmed.edu:s190450/astrocyte_example_wordcount into LocalDockerRegistry
parents 567e7180 0cb47c84
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......@@ -16,7 +16,6 @@ variables:
- env
- ls -laht
- whoami
- set -x
### All base jobs.
......@@ -85,8 +84,8 @@ astrocyte_test:
paths:
- $CI_PROJECT_DIR/workflow/.nextflow.log
# This runs the workflow, opting to use Docker containers.
# This runs the workflow, opting to use Docker containers.
docker_astrocyte_test:
stage: test_docker
variables:
......@@ -95,19 +94,28 @@ docker_astrocyte_test:
script:
- sed -i "s|nextflow_config\x3A \x27biohpc.config\x27|nextflow_config\x3A \x27${config_filename}\x27|" astrocyte_pkg.yml
- echo "Run astrocyte using dockerhub/docker.io registry pulls"
- nextflow -C ./${config_path}/${config_filename} config -flat
- nextflow -C workflow/configs/biohpc_docker.config config -flat | grep -oP "process\.'[\w:]+'\.container = '\K([\w:]+)(?=')" | uniq >> containers.txt
- echo "BUILD_VERSION=hello" >> build.env
- astrocyte_cli run "$CI_PROJECT_DIR" --option=q
- test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
tags:
- cluster_node
artifacts:
paths:
- ./containers.txt
reports:
dotenv: build.env
cache_docker_image:
stage: cache_docker
script:
- echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY
- echo "Pull Docker image from the docker.io registry, re-tag, and push to our GitLab"
- docker
- echo "Need to know what the docker image is ahead of time"
#xargs -a containers.txt -I % docker pull "%"
- xargs -a containers.txt -I % docker tag "%" "$CI_REGISTRY/$CI_PROJECT_ROOT_NAMESPACE/$CI_PROJECT_NAME/%"
- xargs -a containers.txt -I % docker push "$CI_REGISTRY/$CI_PROJECT_ROOT_NAMESPACE/$CI_PROJECT_NAME/%"
needs:
- docker_astrocyte_test
singularity_astrocyte_test:
stage: test_singularity
......
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