mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
Daniel Blankenberg
60 lines
1.8 KiB
Bash
60 lines
1.8 KiB
Bash
#!/bin/sh
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#
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# Script to update UCSC static tables. The idea is to update, but if
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# the update fails, not replace current data/tables with error
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# messages.
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# Edit this line to refer to galaxy's path:
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GALAXY=/galaxy/path
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export PYTHONPATH=${GALAXY}/modules:${GALAXY}/eggs:${GALAXY}/lib
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# setup directories
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mkdir ${GALAXY}/static/ucsc/new
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mkdir ${GALAXY}/static/ucsc/chrom/new
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date
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echo "Updating UCSC static tables."
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# Try to build "builds.txt"
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echo "Updating builds.txt"
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python2.4 ${GALAXY}/cron/parse_builds.py > ${GALAXY}/static/ucsc/new/builds.txt
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if [ $? -eq 0 ]
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then
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cp -uf ${GALAXY}/static/ucsc/new/builds.txt ${GALAXY}/static/ucsc/builds.txt
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else
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echo "Failed to update builds.txt" >&2
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fi
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# Try to build ucsc_build_sites.txt
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echo "Updating ucsc_build_sites.txt"
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python2.4 ${GALAXY}/cron/parse_builds_3_sites.py > ${GALAXY}/static/ucsc/new/ucsc_build_sites.txt
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if [ $? -eq 0 ]
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then
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cp -uf ${GALAXY}/static/ucsc/new/ucsc_build_sites.txt ${GALAXY}/static/ucsc/ucsc_build_sites.txt
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else
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echo "Failed to update builds.txt" >&2
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fi
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# Try to build chromInfo tables
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echo "Building chromInfo tables."
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python2.4 ${GALAXY}/cron/build_chrom_db.py ${GALAXY}/static/ucsc/chrom/new/ ${GALAXY}/static/ucsc/builds.txt
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if [ $? -eq 0 ]
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then
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cp -uf ${GALAXY}/static/ucsc/chrom/new/*.len ${GALAXY}/static/ucsc/chrom/
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else
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echo "Failed to update chromInfo tables." >&2
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fi
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rm -rf ${GALAXY}/static/ucsc/new
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rm -rf ${GALAXY}/static/ucsc/chrom/new
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echo "Update complete."
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#Perform Manual Additions here
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echo "Adding Manual Builds."
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python2.4 ${GALAXY}/cron/add_manual_builds.py ${GALAXY}/static/ucsc/manual_builds.txt ${GALAXY}/static/ucsc/builds.txt ${GALAXY}/static/ucsc/chrom/
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if [ $? -eq 0 ]
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then
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echo "Manual addition was successful."
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else
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echo "Manual addition failed" >&2
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fi |