mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Nate Coraor
92f6ace47f
makes a difference for egg fetching since some eggs are conditional based on config.
58 lines
1.7 KiB
Bash
Executable File
58 lines
1.7 KiB
Bash
Executable File
#!/bin/bash
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# explicitly attempt to fetch eggs before running
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FETCH_EGGS=1
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COPY_SAMPLE_FILES=1
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for arg in "$@"; do
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[ "$arg" = "--skip-eggs" ] && FETCH_EGGS=0
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[ "$arg" = "--stop-daemon" ] && FETCH_EGGS=0
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[ "$arg" = "--skip-samples" ] && COPY_SAMPLE_FILES=0
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done
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SAMPLES="
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config/migrated_tools_conf.xml.sample
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config/shed_tool_conf.xml.sample
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config/shed_tool_data_table_conf.xml.sample
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config/shed_data_manager_conf.xml.sample
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lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
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tool-data/shared/ucsc/builds.txt.sample
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tool-data/shared/ucsc/ucsc_build_sites.txt.sample
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tool-data/shared/igv/igv_build_sites.txt.sample
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tool-data/shared/rviewer/rviewer_build_sites.txt.sample
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tool-data/*.sample
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static/welcome.html.sample
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"
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if [ $COPY_SAMPLE_FILES -eq 1 ]; then
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# Create any missing config/location files
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for sample in $SAMPLES; do
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file=${sample%.sample}
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if [ ! -f "$file" -a -f "$sample" ]; then
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echo "Initializing $file from `basename $sample`"
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cp $sample $file
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fi
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done
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fi
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: ${GALAXY_CONFIG_FILE:=config/galaxy.ini}
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if [ ! -f $GALAXY_CONFIG_FILE ]; then
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GALAXY_CONFIG_FILE=universe_wsgi.ini
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fi
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if [ ! -f $GALAXY_CONFIG_FILE ]; then
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GALAXY_CONFIG_FILE=config/galaxy.ini.sample
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fi
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if [ $FETCH_EGGS -eq 1 ]; then
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python ./scripts/check_eggs.py -q -c $GALAXY_CONFIG_FILE
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if [ $? -ne 0 ]; then
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echo "Some eggs are out of date, attempting to fetch..."
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python ./scripts/fetch_eggs.py -c $GALAXY_CONFIG_FILE
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if [ $? -eq 0 ]; then
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echo "Fetch successful."
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else
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echo "Fetch failed."
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exit 1
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fi
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fi
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fi
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