58 lines
1.3 KiB
Bash
58 lines
1.3 KiB
Bash
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#!/bin/sh
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#
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# Downloads sequence for the rn6 version of R. norvegicus (rat) from
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# UCSC.
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#
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# Note that UCSC's rn6 build has two categories of compressed fasta
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# files:
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#
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# 1. The base files, named chr??.fa.gz
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# 2. The unplaced-sequence files, named chr??_random.fa.gz
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#
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# By default, this script indexes all these files. To change which
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# categories are built by this script, edit the CHRS_TO_INDEX
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# variable below.
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#
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RN6_BASE=ftp://hgdownload.cse.ucsc.edu/goldenPath/rn6/bigZips
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F=rn6.fa.gz
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get() {
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file=$1
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if ! wget --version >/dev/null 2>/dev/null ; then
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if ! curl --version >/dev/null 2>/dev/null ; then
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echo "Please install wget or curl somewhere in your PATH"
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exit 1
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fi
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curl -o `basename $1` $1
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return $?
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else
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wget $1
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return $?
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fi
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}
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HISAT2_BUILD_EXE=./hisat2-build
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if [ ! -x "$HISAT2_BUILD_EXE" ] ; then
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if ! which hisat2-build ; then
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echo "Could not find hisat2-build in current directory or in PATH"
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exit 1
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else
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HISAT2_BUILD_EXE=`which hisat2-build`
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fi
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fi
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rm -f genome.fa
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get ${RN6_BASE}/$F || (echo "Error getting $F" && exit 1)
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gzip -cd $F > genome.fa || (echo "Error unzipping $F" && exit 1)
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rm $F
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CMD="${HISAT2_BUILD_EXE} -p 4 genome.fa genome"
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echo Running $CMD
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if $CMD ; then
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echo "genome index built; you may remove fasta files"
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else
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echo "Index building failed; see error message"
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fi
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