mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
86 lines
3.5 KiB
Bash
86 lines
3.5 KiB
Bash
#!/bin/bash
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set -e
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echo "Deleting galaxy user - it may not exist and this is fine."
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deluser galaxy | true
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: ${GALAXY_TEST_UID:-"1"}
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echo "Creating galaxy group with gid $GALAXY_TEST_UID - it may already exist and this is fine."
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groupadd -r galaxy -g "$GALAXY_TEST_UID" | true
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echo "Creating galaxy user with uid $GALAXY_TEST_UID - it may already exist and this is fine."
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useradd -u $GALAXY_TEST_UID -r -g galaxy -d /home/galaxy -c "Galaxy User" galaxy -s /bin/bash | true
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echo "Setting galaxy user password - the operation may fail."
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echo "galaxy:galaxy" | chpasswd | true
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chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" /galaxy_venv
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: ${GALAXY_TEST_DATABASE_TYPE:-"postgres"}
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if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ];
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then
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su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres
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sleep 3
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GALAXY_TEST_INSTALL_DB_MERGED="true"
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GALAXY_TEST_DBURI="postgres://root@localhost:5930/galaxy?client_encoding=utf8"
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TOOL_SHED_TEST_DBURI="postgres://root@localhost:5930/toolshed?client_encoding=utf8"
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elif [ "$GALAXY_TEST_DATABASE_TYPE" = "mysql" ];
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then
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sh /opt/galaxy/start_mysql.sh
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GALAXY_TEST_INSTALL_DB_MERGED="true"
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GALAXY_TEST_DBURI="mysql://galaxy:galaxy@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock"
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TOOL_SHED_TEST_DBURI="mysql://galaxy:galaxy@localhost/toolshed?unix_socket=/var/run/mysqld/mysqld.sock"
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elif [ "$GALAXY_TEST_DATABASE_TYPE" = "sqlite" ];
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then
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GALAXY_TEST_INSTALL_DB_MERGED="true"
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GALAXY_TEST_DBURI="sqlite:////opt/galaxy/galaxy.sqlite"
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TOOL_SHED_TEST_DBURI="sqlite:////opt/galaxy/toolshed.sqlite"
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chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" /opt/galaxy
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else
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echo "Unknown database type"
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exit 1
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fi
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export GALAXY_TEST_DBURI
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export TOOL_SHED_TEST_DBURI
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export GALAXY_TEST_INSTALL_DB_MERGED
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cd /galaxy
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GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION="$GALAXY_TEST_DBURI";
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export GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION
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TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION="$TOOL_SHED_TEST_DBURI";
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export TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION
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: ${GALAXY_VIRTUAL_ENV:=.venv}
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HOME=/galaxy
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sudo -E -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
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dev_requirements=./lib/galaxy/dependencies/dev-requirements.txt
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[ -f $dev_requirements ] && sudo -E -u "#${GALAXY_TEST_UID}" $GALAXY_VIRTUAL_ENV/bin/pip install -r $dev_requirements
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echo "Upgrading test database..."
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sudo -E -u "#${GALAXY_TEST_UID}" sh manage_db.sh upgrade
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echo "Upgrading tool shed database... $TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION"
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sudo -E -u "#${GALAXY_TEST_UID}" sh manage_db.sh upgrade tool_shed
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if [ -z "$GALAXY_NO_TESTS" ];
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then
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sudo -E -u "#${GALAXY_TEST_UID}" sh run_tests.sh --skip-common-startup $@
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else
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GALAXY_CONFIG_MASTER_API_KEY=${GALAXY_CONFIG_MASTER_API_KEY:-"testmasterapikey"}
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GALAXY_CONFIG_FILE=${GALAXY_CONFIG_FILE:-config/galaxy.ini.sample}
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TOOL_SHED_CONFIG_FILE=${GALAXY_CONFIG_FILE:-config/tool_shed.ini.sample}
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GALAXY_CONFIG_CHECK_MIGRATE_TOOLS=false
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GALAXY_CONFIG_JOB_CONFIG_FILE=${GALAXY_CONFIG_JOB_CONFIG_FILE:-config/job_conf.xml.sample}
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GALAXY_CONFIG_FILE_PATH=${GALAXY_CONFIG_FILE_PATH:-/tmp/gx1}
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GALAXY_CONFIG_NEW_FILE_PATH=${GALAXY_CONFIG_NEW_FILE_PATH:-/tmp/gxtmp}
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export GALAXY_CONFIG_MASTER_API_KEY
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export GALAXY_CONFIG_FILE
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export TOOL_SHED_CONFIG_FILE
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export GALAXY_CONFIG_CHECK_MIGRATE_TOOLS
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export GALAXY_CONFIG_JOB_CONFIG_FILE
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export GALAXY_CONFIG_FILE_PATH
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export GALAXY_CONFIG_NEW_FILE_PATH
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sh run.sh $@
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fi
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