Commit 706e728c authored by Devin OKelly's avatar Devin OKelly
Browse files

Merge branch 'LocalDockerRegistry' of...

Merge branch 'LocalDockerRegistry' of git.biohpc.swmed.edu:s190450/astrocyte_example_wordcount into LocalDockerRegistry
parents 3e4b12b9 ff03378d
......@@ -5,6 +5,7 @@ stages:
- cache_docker
- test_singularity
- cache_singularity
- test_gitlab
variables:
GIT_STRATEGY: clone
......@@ -116,7 +117,7 @@ cache_docker_image:
- xargs -a containers.txt -I % docker push "$CI_REGISTRY/$CI_PROJECT_ROOT_NAMESPACE/$CI_PROJECT_NAME/%"
needs:
- docker_astrocyte_test
singularity_astrocyte_test:
stage: test_singularity
script:
......@@ -126,6 +127,35 @@ singularity_astrocyte_test:
- astrocyte_cli run "$CI_PROJECT_DIR" --option=q
- test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
docker_gitlab_test:
stage: test_gitlab
variables:
config_path : "workflow/configs/"
config_filename : "biohpc_docker_gitlab.config"
script:
- sed -i "s|nextflow_config\x3A \x27biohpc.config\x27|nextflow_config\x3A \x27${config_filename}\x27|" astrocyte_pkg.yml
- astrocyte_cli run "$CI_PROJECT_DIR" --option=q
- test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
tags:
- cluster_node
singularity_gitlab_test:
stage: test_gitlab
variables:
config_path : "workflow/configs/"
config_filename : "biohpc_singularity_gitlab.config"
script:
- export SINGULARITY_DOCKER_USERNAME=${CI_REGISTRY_USER}
- export SINGULARITY_DOCKER_PASSWORD=${CI_REGISTRY_PASSWORD}
- sed -i "s|nextflow_config\x3A \x27biohpc.config\x27|nextflow_config\x3A \x27${config_filename}\x27|" astrocyte_pkg.yml
- astrocyte_cli run "$CI_PROJECT_DIR" --option=q
- test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
tags:
- cluster_node
cache_singularity_image:
stage: cache_singularity
script:
......
docker {
singularity {
enabled = true
runOptions = '--bind /vagrant:/vagrant'
cacheDir = "$baseDir/images/singularity"
......@@ -11,12 +11,12 @@ process {
container = 'git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
}
withName:uppercase {
container = 'git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
container = 'docker://git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
}
withName:tolines {
container = 'git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
container = 'docker://git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
}
withName:wordcounts {
container = 'git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
container = 'docker://git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
}
}
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