remove galaxy submodule and use galaxy 19.09

Author: qianyuanzhu

.gitignore

@@ -0,0 +1 @@
+galaxy/

.gitmodules

@@ -28,19 +28,10 @@ cd <dir>
 git checkout <tag/branch>
 ```
 
-Use git to initialize and clone submodule Galaxy:
+Install Galaxy and dependencies
 
 ```sh
-git submodule init
-git submodule update
-```
-
-Create database and install dependencies required by Galaxy:
-
-```sh
-cd galaxy
-sh install_dependencies.sh 
-sh create_db.sh
+sh install-galaxy.sh
 ```
 
 You will not need to do anything beyond this as all necessary assets are

README.md

@@ -1,7 +1,6 @@
 ---
 cluster: "owens"
 form:
-  - version
   - bc_account
   - bc_num_hours
   - node_type
@@ -38,9 +37,3 @@ attributes:
       - [ "any",     "any"     ]
       - [ "hugemem", "hugemem" ]
       - [ "debug",   "debug"   ]
-  version:
-    widget: select
-    label: "Galaxy  version"
-    help: "This defines the version of Galaxy you want to load."
-    options:
-      - [ "18.05"]

form.yml

@@ -0,0 +1,54 @@
+cd "$(dirname "$0")"
+# Install Galaxy
+if [[ ! -e galaxy ]]; then
+    git clone [email protected]:galaxyproject/galaxy.git
+fi
+
+cd galaxy
+git checkout release_19.09
+
+# Install dependencies
+# Retrieved from line 1-54 in https://github.com/galaxyproject/galaxy/blob/release_19.09/run.sh
+. ./scripts/common_startup_functions.sh
+
+# If there is a file that defines a shell environment specific to this
+# instance of Galaxy, source the file.
+if [ -z "$GALAXY_LOCAL_ENV_FILE" ];
+then
+    GALAXY_LOCAL_ENV_FILE='./config/local_env.sh'
+fi
+
+if [ -f "$GALAXY_LOCAL_ENV_FILE" ];
+then
+    . "$GALAXY_LOCAL_ENV_FILE"
+fi
+
+GALAXY_PID=${GALAXY_PID:-galaxy.pid}
+GALAXY_LOG=${GALAXY_LOG:-galaxy.log}
+PID_FILE=$GALAXY_PID
+LOG_FILE=$GALAXY_LOG
+
+parse_common_args $@
+
+run_common_start_up
+
+setup_python
+
+if [ ! -z "$GALAXY_RUN_WITH_TEST_TOOLS" ];
+then
+    export GALAXY_CONFIG_OVERRIDE_TOOL_CONFIG_FILE="test/functional/tools/samples_tool_conf.xml"
+    export GALAXY_CONFIG_ENABLE_BETA_WORKFLOW_MODULES="true"
+    export GALAXY_CONFIG_OVERRIDE_ENABLE_BETA_TOOL_FORMATS="true"
+    export GALAXY_CONFIG_OVERRIDE_WEBHOOKS_DIR="test/functional/webhooks"
+fi
+
+if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then
+    python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR"
+fi
+
+set_galaxy_config_file_var
+
+if [ "$INITIALIZE_TOOL_DEPENDENCIES" -eq 1 ]; then
+    # Install Conda environment if needed.
+    python ./scripts/manage_tool_dependencies.py init_if_needed
+fi

galaxy

@@ -4,7 +4,7 @@ category: Interactive Apps
 subcategory: Servers
 role: batch_connect
 description: |
-  This app will launch [Galaxy] on the [Owens cluster].
+  This app will launch [Galaxy 19.09] on the [Owens cluster].
 
   [Galaxy]: https://galaxyproject.org/
   [Owens cluster]: https://www.osc.edu/resources/technical_support/supercomputers/owens

install-galaxy.sh

@@ -1,5 +1,11 @@
 <%-
-  props = ":ppn=1"
+  ppn   = num_cores.blank? ? 28 : num_cores.to_i
+  props = case node_type
+          when "hugemem"
+            ":ppn=48"
+          else
+            ":ppn=#{ppn}"
+          end
 -%>
 ---
 batch_connect:

manifest.yml

@@ -4,3 +4,83 @@
 # Find available port to run server on
 port=8080
 
+# Define Galaxy Variables
+export GALAXY_PATH="<%= BatchConnect::App.from_token(session.token).root.realpath.join("galaxy").to_s %>"
+export GALAXY_CONFIG_FILE="${PWD}/galaxy.yml"
+MOUNT="/node/${HOSTNAME}/8080=galaxy.webapps.galaxy.buildapp:uwsgi_app()"
+DATAROOT=${HOME}/.galaxy
+EMAIL="${USER}@osc.edu"
+export JOB_CONFIG_FILE_PATH="${PWD}/job_conf.xml"
+
+echo "GALAXY location: '${GALAXY_PATH}'"
+echo "Data location: '${DATAROOT}'"
+
+# Load the required environment
+<%-
+  if context.node_type=="hugemem"
+      ppn = 48
+  elsif context.num_cores.blank?
+      ppn = 28
+  else
+      ppn = context.num_cores.to_i
+  end
+-%>
+
+# Generate Galaxy job configuration file
+(
+umask 077
+cat > "${JOB_CONFIG_FILE_PATH}" << EOL
+<?xml version="1.0"?>
+<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
+<job_conf>
+    <plugins>
+        <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner"/>
+    </plugins>
+    <destinations default="pbs_default">
+        <destination id="pbs_default" runner="pbs">
+            <param id="Resource_List">walltime=5:00:00,nodes=1:ppn=<%= ppn %></param>
+            <param id="-p">128</param>
+        </destination>
+        <destination id="other_cluster" runner="pbs">
+            <param id="destination">@other.cluster</param>
+        </destination>
+        <destination id="long_jobs" runner="pbs">
+            <param id="Resource_List">walltime=5:00:00,nodes=1:ppn=1</param>
+            <param id="-p">128</param>
+            <param id="Output_Path"></param>
+        </destination>
+    </destinations>
+</job_conf>
+EOL
+)
+
+# Generate Galaxy configuration file
+(
+umask 077
+cat > "${GALAXY_CONFIG_FILE}" << EOL
+uwsgi:
+  http: 0.0.0.0:8080
+  buffer-size: 16384
+  processes: 1
+  threads: 4
+  offload-threads: 2
+  static-map: /static/style=static/style/blue
+  static-map: /static=static
+  static-map: /favicon.ico=static/favicon.ico
+  master: false
+  virtualenv: .venv
+  pythonpath: lib
+  mount: ${MOUNT}
+  manage-script-name: true
+  thunder-lock: false
+  die-on-term: true
+  hook-master-start: unix_signal:2 gracefully_kill_them_all
+  hook-master-start: unix_signal:15 gracefully_kill_them_all
+  py-call-osafterfork: true
+  enable-threads: true
+galaxy:
+  data_dir: ${DATAROOT}
+  single_user: ${EMAIL}
+  tool_dependency_dir: ${GALAXY_PATH}/database/dependencies
+EOL
+)