clean up Dockerfile

Dockerfile

@@ -19,13 +19,11 @@ RUN apt-get update && apt-get install -y yarn
 COPY job_conf.xml /app/galaxy/config/job_conf.xml
 COPY dependency_resolvers_conf.xml /app/galaxy/config/dependency_resolvers_conf.xml
 COPY galaxy.yml /app/galaxy/config/galaxy.yml
-COPY welcome.html /app/galaxy/static/welcome.html
 COPY tool_conf.xml /app/galaxy/config/tool_conf.xml
-#COPY init_galaxy.sh /app/galaxy/init_galaxy.sh
 RUN cd /app/galaxy && ./scripts/common_startup.sh 
-#RUN cd /app/galaxy && . .venv/bin/activate && pip install cwltool==1.0.20181012180214
 RUN cd /app/galaxy && ls database/*
 RUN cd /app/galaxy && ./create_db.sh
 RUN cd /app/galaxy && ./manage_db.sh upgrade
+COPY welcome.html /app/galaxy/static/welcome.html
 CMD ["sh", "/app/galaxy/run.sh"]
 EXPOSE 8080

init_galaxy.sh

-#!/bin/sh
-
-
-# Usage: ./run.sh <start|stop|restart>
-#
-#
-# Description: This script can be used to start or stop the galaxy
-# web application.
-
-cd "$(dirname "$0")"
-
-. ./scripts/common_startup_functions.sh
-
-# If there is a file that defines a shell environment specific to this
-# instance of Galaxy, source the file.
-if [ -z "$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_ENABLE_BETA_WORKFLOW_FORMAT="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