mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
mvdbeek
98 lines
2.9 KiB
Bash
98 lines
2.9 KiB
Bash
#!/bin/sh
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#
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# Script to update UCSC shared data 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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## Change the Galaxy path on the next line if needed:
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GALAXY=$(dirname "$0")/..
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GALAXY_VIRTUAL_ENV="${GALAXY_VIRTUAL_ENV:-$GALAXY/.venv}"
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if [ -d "$GALAXY_VIRTUAL_ENV" ]; then
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echo "Activating virtualenv at $GALAXY_VIRTUAL_ENV"
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. "$GALAXY_VIRTUAL_ENV/bin/activate"
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fi
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PYTHONPATH=${GALAXY}/lib
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export PYTHONPATH
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# Setup directories
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echo "Creating required directories."
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DIRS="
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${GALAXY}/tool-data/shared/ucsc/new
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${GALAXY}/tool-data/shared/ucsc/chrom
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${GALAXY}/tool-data/shared/ucsc/chrom/new
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"
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for dir in $DIRS; do
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if [ ! -d "$dir" ]; then
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echo "Creating $dir"
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mkdir "$dir"
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else
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echo "$dir already exists, continuing."
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fi
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done
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date
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echo "Updating UCSC shared data tables."
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# Try to build "builds.txt"
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echo "Updating builds.txt"
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python "${GALAXY}/cron/parse_builds.py" > "${GALAXY}/tool-data/shared/ucsc/new/builds.txt"
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if [ $? -eq 0 ]
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then
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diff "${GALAXY}/tool-data/shared/ucsc/new/builds.txt" "${GALAXY}/tool-data/shared/ucsc/builds.txt" > /dev/null 2>&1
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if [ $? -ne 0 ]
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then
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cp -f "${GALAXY}/tool-data/shared/ucsc/new/builds.txt" "${GALAXY}/tool-data/shared/ucsc/builds.txt"
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fi
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else
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echo "Failed to update builds.txt" >&2
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fi
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# Try to build ucsc_build_sites.txt
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echo "Updating ucsc_build_sites.txt"
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python "${GALAXY}/cron/parse_builds_3_sites.py" > "${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt"
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if [ $? -eq 0 ]
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then
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diff "${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt" "${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt" > /dev/null 2>&1
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if [ $? -ne 0 ]
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then
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cp -f "${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt" "${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt"
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fi
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else
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echo "Failed to update ucsc_build_sites.txt" >&2
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fi
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# Try to build chromInfo tables
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echo "Building chromInfo tables."
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python "${GALAXY}/cron/build_chrom_db.py" "${GALAXY}/tool-data/shared/ucsc/chrom/new/" "${GALAXY}/tool-data/shared/ucsc/builds.txt"
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if [ $? -eq 0 ]
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then
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for src in "${GALAXY}"/tool-data/shared/ucsc/chrom/new/*.len
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do
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dst=${GALAXY}/tool-data/shared/ucsc/chrom/$(basename "$src")
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diff "$src" "$dst" > /dev/null 2>&1
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if [ $? -ne 0 ]
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then
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echo "cp -f \"$src\" \"$dst\""
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cp -f "$src" "$dst"
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fi
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done
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else
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echo "Failed to update chromInfo tables." >&2
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fi
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rm -rf "${GALAXY}/tool-data/shared/ucsc/new"
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rm -rf "${GALAXY}/tool-data/shared/ucsc/chrom/new"
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echo "Update complete."
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# Perform Manual Additions here
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echo "Adding Manual Builds."
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python "${GALAXY}/cron/add_manual_builds.py" "${GALAXY}/tool-data/shared/ucsc/manual_builds.txt" "${GALAXY}/tool-data/shared/ucsc/builds.txt" "${GALAXY}/tool-data/shared/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
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