changed execution order in startup and added test for data persistence

.github/workflows/single.sh

@@ -48,6 +48,11 @@ cd "$WORKING_DIR"
 docker build -t quay.io/bgruening/galaxy galaxy/
 #container_size_check   quay.io/bgruening/galaxy  1500
 
+echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin "$DOCKER_REGISTRY"
+docker tag quay.io/bgruening/galaxy jyotipm29/galaxy-stable:latest
+docker push jyotipm29/galaxy-stable:latest
+docker logout "$DOCKER_REGISTRY"
+
 mkdir local_folder
 docker run -d -p 8080:80 -p 8021:21 -p 8022:22 \
     --name galaxy \
@@ -133,6 +138,28 @@ docker_exec install-tools "$SAMPLE_TOOLS"
 # Test the Conda installation
 docker_exec_run bash -c 'export PATH=$GALAXY_CONFIG_TOOL_DEPENDENCY_DIR/_conda/bin/:$PATH && conda --version && conda install samtools -c bioconda --yes'
 
+# Test if data persistence works
+docker stop galaxy
+docker rm -f galaxy
+
+cd "$WORKING_DIR"
+docker run -d -p 8080:80 \
+    --name galaxy \
+    --privileged=true \
+    -v "$(pwd)/local_folder:/export/" \
+    -e GALAXY_CONFIG_ALLOW_USER_DATASET_PURGE=True \
+    -e GALAXY_CONFIG_ALLOW_PATH_PASTE=True \
+    -e GALAXY_CONFIG_ALLOW_USER_DELETION=True \
+    -e GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES=True \
+    -v /tmp/:/tmp/ \
+    quay.io/bgruening/galaxy
+
+echo 'Waiting for Galaxy to come up.'
+galaxy-wait -g $BIOBLEND_GALAXY_URL --timeout 600
+
+# Test if the tool installed previously is available
+curl -v --fail 'http://localhost:8080/api/tools/toolshed.g2.bx.psu.edu/repos/devteam/cut_columns/Cut1/1.0.2'
+
 # analyze image using dive tool
 CI=true dive quay.io/bgruening/galaxy
 

.github/workflows/single_container.yml

@@ -14,3 +14,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Build and Test
       run: bash .github/workflows/single.sh
+      env:
+        DOCKER_REGISTRY: ${{ secrets.docker_registry }}
+        DOCKER_USERNAME: ${{ secrets.docker_registry_username }}
+        DOCKER_PASSWORD: ${{ secrets.docker_registry_password }}

galaxy/startup.sh

@@ -319,15 +319,6 @@ function start_supervisor {
         fi
     fi
 
-    wait_for_postgres
-
-    # Make sure the database is automatically updated
-    if [[ ! -z $GALAXY_AUTO_UPDATE_DB ]]
-    then
-        echo "Updating Galaxy database"
-        sh manage_db.sh -c $GALAXY_CONFIG_FILE upgrade
-    fi
-
     if [[ ! -z $SUPERVISOR_MANAGE_CRON ]]; then
         if [[ $NONUSE != *"cron"* ]]
         then
@@ -496,16 +487,16 @@ if $PRIVILEGED; then
     if [[ -z $DOCKER_PARENT ]]; then
         #build the docker in docker environment
         bash /root/cgroupfs_mount.sh
-        start_gravity
         start_supervisor
+        start_gravity
         supervisorctl start docker
         wait_for_docker
     else
         #inheriting /var/run/docker.sock from parent, assume that you need to
         #run docker with sudo to validate
         echo "$GALAXY_USER ALL = NOPASSWD : ALL" >> /etc/sudoers
-        start_gravity
         start_supervisor
+        start_gravity
     fi
     if  [[ ! -z $PULL_IT_IMAGES ]]; then
         echo "About to pull IT images. Depending on the size, this may take a while!"
@@ -523,8 +514,17 @@ if $PRIVILEGED; then
 else
     echo "Disable Galaxy Interactive Tools. Start with --privileged to enable ITs."
     export GALAXY_CONFIG_INTERACTIVETOOLS_ENABLE=False
-    start_gravity
     start_supervisor
+    start_gravity
+fi
+
+wait_for_postgres
+
+# Make sure the database is automatically updated
+if [[ ! -z $GALAXY_AUTO_UPDATE_DB ]]
+then
+    echo "Updating Galaxy database"
+    sh manage_db.sh -c $GALAXY_CONFIG_FILE upgrade
 fi
 
 # In case the user wants the default admin to be created, do so.