add gitlab-ci.yml

.gitlab-ci.yml

+stages:
+  - build
+  - check
+  - create
+  - update
+
+image: docker:stable
+
+services:
+  - docker:dind
+  
+variables:
+  DOCKER_HOST: tcp://docker:2376
+  DOCKER_TLS_CERTDIR: "/certs"
+  PLANEMO_IMAGE_TAG: registry.forgemia.inra.fr/record/docker-planemo/docker-planemo-singularity:0.74.1
+  GALAXY_WRAPPER: siwaa_recipe/galaxy_tools/tools_AZODYN.xml
+    
+build azodyn:
+  stage: build
+  
+  variables:
+    IMAGE_TAG: $CI_REGISTRY/$CI_PROJECT_NAMESPACE/azodyn_pea:$CI_COMMIT_SHA
+  
+  script:
+    - docker info
+    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+    - docker pull $IMAGE_TAG || true
+    - docker build --cache-from $IMAGE_TAG -t $IMAGE_TAG -f siwaa_recipe/container/Dockerfile .
+    - docker push $IMAGE_TAG
+    
+  when: manual
+
+check azodyn:
+  stage: check
+  
+  script:
+    - docker run $PLANEMO_IMAGE_TAG --version
+    - head $GALAXY_WRAPPER
+    - |- 
+        sed -i.bak "s|:latest|:$$CI_COMMIT_SHA</container>|g" $GALAXY_WRAPPER
+    - head $GALAXY_WRAPPER
+    - docker run --privileged -v $PWD:/galaxy-central $PLANEMO_IMAGE_TAG lint --report_level error $GALAXY_WRAPPER
+    - docker run --privileged -v $PWD:/galaxy-central -e SINGULARITY_DOCKER_USERNAME=$SINGULARITY_DOCKER_USERNAME -e SINGULARITY_DOCKER_PASSWORD=$SINGULARITY_DOCKER_PASSWORD $PLANEMO_IMAGE_TAG test --no_cleanup --install_galaxy --galaxy_branch release_21.09 --job_config_file siwaa_recipe/job_conf.xml $GALAXY_WRAPPER
+  artifacts:
+    paths:
+      - tool_test_output.html
+      - tool_test_output.json
+    when: always
+
+  when: manual
+  
+create azodyn:
+  stage: create
+
+  script:
+    - docker run $PLANEMO_IMAGE_TAG --version
+    - head $GALAXY_WRAPPER
+    - |- 
+        sed -i.bak "s|:latest|:$$CI_COMMIT_SHA</container>|g" $GALAXY_WRAPPER
+    - head $GALAXY_WRAPPER
+    - docker run --privileged -v $PWD:/galaxy-central $PLANEMO_IMAGE_TAG shed_create --shed_target https://toolshed-siwaa.toulouse.inrae.fr --shed_key $SHED_KEY siwaa_recipe/galaxy_tools
+
+  when: manual
+  
+#  script:
+#    - planemo --version
+#    - echo $SHED_EMAIL
+#    - echo $SHED_PASSWORD
+#    - planemo shed_create --shed_target "https://toolshed-siwaa.toulouse.inrae.fr/" --shed_email "$SHED_EMAIL" --shed_password "$SHED_PASSWORD" siwaa_recipe/galaxy_tools
+#    - planemo shed_create --shed_target https://toolshed-siwaa.toulouse.inrae.fr --shed_email siwaa-support@inrae.fr --shed_password AQJCZw6BZqxrC9P siwaa_recipe/galaxy_tools
+    
+#  when: manual 
+
+update azodyn:
+  stage: update
+
+  script:
+    - docker run $PLANEMO_IMAGE_TAG --version
+    - head $GALAXY_WRAPPER
+    - |- 
+        if [[ $CI_TOOL_TEST_IMAGE != "" ]]; then
+          sed -i.bak "s|:latest|:$$CI_COMMIT_SHA</container>|g" $GALAXY_WRAPPER
+        fi
+    - head $GALAXY_WRAPPER
+    - docker run --privileged -v $PWD:/galaxy-central $PLANEMO_IMAGE_TAG shed_update --shed_target https://toolshed-siwaa.toulouse.inrae.fr --shed_key $SHED_KEY siwaa_recipe/galaxy_tools
+
+  when: manual

siwaa_recipe/job_conf.xml

@@ -6,7 +6,7 @@
     </plugins>
     <destinations>
       <destination id="local" runner="local">
-	<param id="singularity_enabled">true</param>
+	      <param id="singularity_enabled">true</param>
       </destination>
     </destinations>
 </job_conf>