[2] | 1 | #!/bin/sh |
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| 2 | # |
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| 3 | # Script to update UCSC shared data tables. The idea is to update, but if |
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| 4 | # the update fails, not replace current data/tables with error |
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| 5 | # messages. |
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| 6 | |
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| 7 | # Edit this line to refer to galaxy's path: |
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| 8 | GALAXY=/galaxy/path |
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| 9 | PYTHONPATH=${GALAXY}/lib |
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| 10 | export PYTHONPATH |
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| 11 | |
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| 12 | # setup directories |
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| 13 | echo "Creating required directories." |
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| 14 | DIRS=" |
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| 15 | ${GALAXY}/tool-data/shared/ucsc/new |
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| 16 | ${GALAXY}/tool-data/shared/ucsc/chrom |
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| 17 | ${GALAXY}/tool-data/shared/ucsc/chrom/new |
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| 18 | " |
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| 19 | for dir in $DIRS; do |
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| 20 | if [ ! -d $dir ]; then |
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| 21 | echo "Creating $dir" |
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| 22 | mkdir $dir |
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| 23 | else |
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| 24 | echo "$dir already exists, continuing." |
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| 25 | fi |
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| 26 | done |
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| 27 | |
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| 28 | date |
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| 29 | echo "Updating UCSC shared data tables." |
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| 30 | |
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| 31 | # Try to build "builds.txt" |
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| 32 | echo "Updating builds.txt" |
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| 33 | python ${GALAXY}/cron/parse_builds.py > ${GALAXY}/tool-data/shared/ucsc/new/builds.txt |
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| 34 | if [ $? -eq 0 ] |
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| 35 | then |
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| 36 | diff ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt > /dev/null 2>&1 |
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| 37 | if [ $? -ne 0 ] |
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| 38 | then |
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| 39 | cp -f ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt |
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| 40 | fi |
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| 41 | else |
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| 42 | echo "Failed to update builds.txt" >&2 |
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| 43 | fi |
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| 44 | |
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| 45 | # Try to build ucsc_build_sites.txt |
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| 46 | echo "Updating ucsc_build_sites.txt" |
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| 47 | python ${GALAXY}/cron/parse_builds_3_sites.py > ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt |
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| 48 | if [ $? -eq 0 ] |
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| 49 | then |
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| 50 | 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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| 51 | if [ $? -ne 0 ] |
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| 52 | then |
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| 53 | 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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| 54 | fi |
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| 55 | else |
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| 56 | echo "Failed to update builds.txt" >&2 |
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| 57 | fi |
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| 58 | |
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| 59 | # Try to build chromInfo tables |
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| 60 | echo "Building chromInfo tables." |
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| 61 | 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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| 62 | if [ $? -eq 0 ] |
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| 63 | then |
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| 64 | for src in ${GALAXY}/tool-data/shared/ucsc/chrom/new/*.len |
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| 65 | do |
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| 66 | dst=${GALAXY}/tool-data/shared/ucsc/chrom/`basename $src` |
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| 67 | diff $src $dst > /dev/null 2>&1 |
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| 68 | if [ $? -ne 0 ] |
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| 69 | then |
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| 70 | echo "cp -f $src $dst" |
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| 71 | cp -f $src $dst |
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| 72 | fi |
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| 73 | done |
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| 74 | else |
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| 75 | echo "Failed to update chromInfo tables." >&2 |
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| 76 | fi |
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| 77 | |
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| 78 | rm -rf ${GALAXY}/tool-data/shared/ucsc/new |
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| 79 | rm -rf ${GALAXY}/tool-data/shared/ucsc/chrom/new |
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| 80 | echo "Update complete." |
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| 81 | |
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| 82 | #Perform Manual Additions here |
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| 83 | echo "Adding Manual Builds." |
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| 84 | 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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| 85 | if [ $? -eq 0 ] |
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| 86 | then |
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| 87 | echo "Manual addition was successful." |
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| 88 | else |
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| 89 | echo "Manual addition failed" >&2 |
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| 90 | fi |
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