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https://github.com/galaxyproject/galaxy.git
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75 lines
1.5 KiB
Bash
75 lines
1.5 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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esac
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LINKS="
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/depot/data2/galaxy/alignseq.loc
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/depot/data2/galaxy/binned_scores.loc
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/depot/data2/galaxy/blastdb.loc
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/depot/data2/galaxy/bowtie_indices.loc
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/depot/data2/galaxy/encode_datasets.loc
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/depot/data2/galaxy/lastz_seqs.loc
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/depot/data2/galaxy/liftOver.loc
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/depot/data2/galaxy/maf_index.loc
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/depot/data2/galaxy/maf_pairwise.loc
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/depot/data2/galaxy/microbes/microbial_data.loc
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/depot/data2/galaxy/phastOdds.loc
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/depot/data2/galaxy/quality_scores.loc
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/depot/data2/galaxy/regions.loc
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/depot/data2/galaxy/sam_fa_indices.loc
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/depot/data2/galaxy/sequence_index_base.loc
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/depot/data2/galaxy/sequence_index_color.loc
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/depot/data2/galaxy/taxonomy
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/depot/data2/galaxy/twobit.loc
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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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"
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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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for link in $LINKS; do
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echo "Linking $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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ln -sf $HYPHY tool-data/HYPHY
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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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python ./scripts/fetch_eggs.py all
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