[2] | 1 | #!/bin/sh |
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| 2 | |
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| 3 | cd `dirname $0` |
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| 4 | |
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| 5 | : ${HOSTTYPE:=`uname -m`} |
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| 6 | |
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| 7 | # link to HYPHY is arch-dependent |
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| 8 | case "$OSTYPE" in |
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| 9 | linux-gnu) |
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| 10 | kernel=`uname -r | cut -f1,2 -d.` |
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| 11 | HYPHY="/galaxy/software/linux$kernel-$HOSTTYPE/hyphy" |
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| 12 | ;; |
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| 13 | darwin*) |
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| 14 | this_minor=`uname -r | awk -F. '{print ($1-4)}'` |
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| 15 | machine=`machine` |
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| 16 | for minor in `jot - 3 $this_minor 1`; do |
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| 17 | HYPHY="/galaxy/software/macosx10.$minor-$machine/hyphy" |
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| 18 | [ -d "$HYPHY" ] && break |
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| 19 | done |
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| 20 | [ ! -d "$HYPHY" ] && unset HYPHY |
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| 21 | ;; |
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| 22 | solaris2.10) |
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| 23 | # For the psu-production builder which is Solaris, but jobs run on a |
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| 24 | # Linux cluster |
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| 25 | HYPHY="/galaxy/software/linux2.6-x86_64/hyphy" |
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| 26 | ;; |
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| 27 | esac |
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| 28 | |
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| 29 | LINKS=" |
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| 30 | /galaxy/data/location/add_scores.loc |
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| 31 | /galaxy/data/location/alignseq.loc |
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| 32 | /galaxy/data/annotation_profiler |
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| 33 | /galaxy/data/annotation_profiler/annotation_profiler.loc |
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| 34 | /galaxy/data/annotation_profiler/annotation_profiler_options.xml |
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| 35 | /galaxy/data/annotation_profiler/annotation_profiler_valid_builds.txt |
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| 36 | /galaxy/data/location/bfast_indexes.loc |
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| 37 | /galaxy/data/location/binned_scores.loc |
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| 38 | /galaxy/data/location/blastdb.loc |
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| 39 | /galaxy/data/location/bowtie_indices.loc |
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| 40 | /galaxy/data/location/bowtie_indices_color.loc |
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| 41 | /galaxy/data/location/bwa_index.loc |
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| 42 | /galaxy/data/location/codingSnps.loc |
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| 43 | /galaxy/data/location/encode_datasets.loc |
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| 44 | /galaxy/home/universe/encode_feature_partitions |
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| 45 | /galaxy/data/location/lastz_seqs.loc |
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| 46 | /galaxy/data/location/liftOver.loc |
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| 47 | /galaxy/data/location/maf_index.loc |
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| 48 | /galaxy/data/location/maf_pairwise.loc |
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| 49 | /galaxy/data/location/microbes/microbial_data.loc |
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| 50 | /galaxy/data/location/perm_base_index.loc |
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| 51 | /galaxy/data/location/perm_color_index.loc |
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| 52 | /galaxy/data/location/phastOdds.loc |
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| 53 | /galaxy/data/location/quality_scores.loc |
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| 54 | /galaxy/data/location/regions.loc |
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| 55 | /galaxy/data/location/sam_fa_indices.loc |
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| 56 | /galaxy/data/location/srma_index.loc |
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| 57 | /galaxy/data/taxonomy |
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| 58 | /galaxy/data/location/twobit.loc |
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| 59 | " |
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| 60 | |
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| 61 | SAMPLES=" |
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| 62 | datatypes_conf.xml.sample |
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| 63 | universe_wsgi.ini.sample |
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| 64 | tool_data_table_conf.xml.sample |
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| 65 | tool-data/shared/ucsc/builds.txt.sample |
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| 66 | " |
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| 67 | |
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| 68 | DIRS=" |
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| 69 | database |
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| 70 | database/files |
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| 71 | database/tmp |
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| 72 | database/compiled_templates |
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| 73 | database/job_working_directory |
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| 74 | database/import |
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| 75 | database/pbs |
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| 76 | " |
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| 77 | |
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| 78 | JARS="/galaxy/software/jars" |
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| 79 | |
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| 80 | for link in $LINKS; do |
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| 81 | echo "Linking $link" |
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| 82 | rm -f tool-data/`basename $link` |
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| 83 | ln -sf $link tool-data |
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| 84 | done |
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| 85 | |
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| 86 | if [ -d "$HYPHY" ]; then |
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| 87 | echo "Linking $HYPHY" |
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| 88 | rm -f tool-data/HYPHY |
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| 89 | ln -sf $HYPHY tool-data/HYPHY |
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| 90 | fi |
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| 91 | |
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| 92 | if [ -d "$JARS" ]; then |
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| 93 | echo "Linking $JARS" |
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| 94 | rm -f tool-data/shared/jars |
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| 95 | ln -sf $JARS tool-data/shared/jars |
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| 96 | fi |
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| 97 | |
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| 98 | for sample in $SAMPLES; do |
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| 99 | file=`echo $sample | sed -e 's/\.sample$//'` |
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| 100 | echo "Copying $sample to $file" |
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| 101 | cp $sample $file |
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| 102 | done |
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| 103 | |
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| 104 | for dir in $DIRS; do |
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| 105 | if [ ! -d $dir ]; then |
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| 106 | echo "Creating $dir" |
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| 107 | mkdir $dir |
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| 108 | fi |
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| 109 | done |
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| 110 | |
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| 111 | # for wig_to_bigWig |
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| 112 | if [ ! -f "tool-data/shared/ucsc/chrom/hg17.len" -a -f "test-data/wig_to_bigwig_hg17.len" ]; then |
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| 113 | mkdir -p tool-data/shared/ucsc/chrom |
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| 114 | cp test-data/wig_to_bigwig_hg17.len tool-data/shared/ucsc/chrom/hg17.len |
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| 115 | fi |
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| 116 | |
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| 117 | python ./scripts/fetch_eggs.py all |
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