mirror of
https://github.com/galaxyproject/galaxy.git
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144 lines
3.9 KiB
Bash
144 lines
3.9 KiB
Bash
#!/bin/sh
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cd `dirname $0`
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: ${HOSTTYPE:=`uname -m`}
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# link to HYPHY is arch-dependent
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case "$OSTYPE" in
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linux-gnu)
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kernel=`uname -r | cut -f1,2 -d.`
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HYPHY="/galaxy/software/linux$kernel-$HOSTTYPE/hyphy"
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;;
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darwin*)
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this_minor=`uname -r | awk -F. '{print ($1-4)}'`
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machine=`machine`
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for minor in `jot - 3 $this_minor 1`; do
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HYPHY="/galaxy/software/macosx10.$minor-$machine/hyphy"
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[ -d "$HYPHY" ] && break
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done
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[ ! -d "$HYPHY" ] && unset HYPHY
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;;
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solaris2.10)
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# For the psu-production builder which is Solaris, but jobs run on a
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# Linux cluster
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HYPHY="/galaxy/software/linux2.6-x86_64/hyphy"
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;;
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esac
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LINKS="
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/galaxy/data/location/add_scores.loc
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/galaxy/data/location/all_fasta.loc
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/galaxy/data/location/alignseq.loc
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/galaxy/data/annotation_profiler
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/galaxy/data/annotation_profiler/annotation_profiler.loc
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/galaxy/data/annotation_profiler/annotation_profiler_options.xml
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/galaxy/data/annotation_profiler/annotation_profiler_valid_builds.txt
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/galaxy/data/location/bfast_indexes.loc
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/galaxy/data/location/binned_scores.loc
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/galaxy/data/location/blastdb.loc
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/galaxy/data/location/bowtie_indices.loc
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/galaxy/data/location/bowtie_indices_color.loc
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/galaxy/data/location/bwa_index.loc
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/galaxy/data/location/bwa_index_color.loc
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/galaxy/data/location/ccat_configurations.loc
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/galaxy/data/location/codingSnps.loc
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/galaxy/data/location/encode_datasets.loc
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/galaxy/home/universe/encode_feature_partitions
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/galaxy/data/location/lastz_seqs.loc
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/galaxy/data/location/liftOver.loc
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/galaxy/data/location/maf_index.loc
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/galaxy/data/location/maf_pairwise.loc
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/galaxy/data/location/microbial_data.loc
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/galaxy/data/location/mosaik_index.loc
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/galaxy/data/location/perm_base_index.loc
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/galaxy/data/location/perm_color_index.loc
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/galaxy/data/location/phastOdds.loc
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/galaxy/data/location/picard_index.loc
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/galaxy/data/location/quality_scores.loc
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/galaxy/data/location/regions.loc
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/galaxy/data/location/sam_fa_indices.loc
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/galaxy/data/location/srma_index.loc
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/galaxy/data/taxonomy
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/galaxy/data/location/twobit.loc
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/galaxy/software/tool-data/gatk
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"
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SAMPLES="
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datatypes_conf.xml.sample
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universe_wsgi.ini.sample
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tool_data_table_conf.xml.sample
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tool-data/shared/ucsc/builds.txt.sample
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migrated_tools_conf.xml.sample
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"
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DIRS="
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database
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database/files
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database/tmp
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database/compiled_templates
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database/job_working_directory
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database/import
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database/pbs
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"
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JARS="/galaxy/software/jars"
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for link in $LINKS; do
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echo "Linking $link"
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rm -f tool-data/`basename $link`
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ln -sf $link tool-data
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done
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if [ -d "$HYPHY" ]; then
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echo "Linking $HYPHY"
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rm -f tool-data/HYPHY
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ln -sf $HYPHY tool-data/HYPHY
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fi
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if [ -d "$JARS" ]; then
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echo "Linking $JARS"
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rm -f tool-data/shared/jars
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ln -sf $JARS tool-data/shared/jars
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fi
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for sample in $SAMPLES; do
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file=`echo $sample | sed -e 's/\.sample$//'`
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echo "Copying $sample to $file"
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cp $sample $file
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done
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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 $dir
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fi
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done
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# for wig_to_bigWig and bed_to_bigBed
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for build in hg17 hg18; do
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if [ -f "test-data/chrom/$build.len" ]; then
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echo "Copying test-data/chrom/$build.len to tool-data/shared/ucsc/chrom/"
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mkdir -p tool-data/shared/ucsc/chrom
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cp test-data/chrom/$build.len tool-data/shared/ucsc/chrom/$build.len
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fi
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done
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if [ -d "test-data-repo" ]; then
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echo "Updating test data repository"
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cd test-data-repo
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hg pull
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hg update
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cd ..
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else
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echo "Cloning test data repository"
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hg clone http://bitbucket.org/natefoo/galaxy-test-data/ test-data-repo
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fi
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echo "Setting up test data location files"
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python test-data-repo/location/make_location.py
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echo "Appending tool-data/shared/ucsc/builds.txt.buildbot to tool-data/shared/ucsc/builds.txt"
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cat tool-data/shared/ucsc/builds.txt.buildbot >> tool-data/shared/ucsc/builds.txt
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python ./scripts/fetch_eggs.py all
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