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Hervé MENAGER
galaxy-cwl-is-docker
Commits
73318092
Commit
73318092
authored
Apr 01, 2019
by
Hervé MENAGER
Browse files
clean up Dockerfile
parent
b711dfe9
Changes
2
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Dockerfile
View file @
73318092
...
...
@@ -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
deleted
100755 → 0
View file @
b711dfe9
#!/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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