Merge branch 'LocalDockerRegistry' of...

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

.gitlab-ci.yml

@@ -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