Merge branch 'LocalDockerRegistry' of...

Merge branch 'LocalDockerRegistry' of git.biohpc.swmed.edu:s190450/astrocyte_example_wordcount into LocalDockerRegistry

.gitlab-ci.yml

@@ -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:

workflow/configs/biohpc_singularity_gitlab.config

-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'
     }
 }