Commit 73318092 authored by Hervé  MENAGER's avatar Hervé MENAGER

clean up Dockerfile

parent b711dfe9
......@@ -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
#!/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
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