90 lines
1.4 KiB
Bash
90 lines
1.4 KiB
Bash
#!/bin/sh
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#
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# Builds an index from UMD Freeze 3.0 of the Bos Taurus (cow) genome.
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#
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BASE_CHRS="\
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Chr1 \
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Chr2 \
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Chr3 \
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Chr4 \
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Chr5 \
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Chr6 \
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Chr7 \
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Chr8 \
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Chr9 \
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Chr10 \
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Chr11 \
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Chr12 \
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Chr13 \
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Chr14 \
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Chr15 \
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Chr16 \
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Chr17 \
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Chr18 \
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Chr19 \
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Chr20 \
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Chr21 \
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Chr22 \
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Chr23 \
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Chr24 \
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Chr25 \
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Chr26 \
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Chr27 \
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Chr28 \
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Chr29 \
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ChrX \
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ChrU \
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ChrY-contigs \
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ChrY-contigs.SHOTGUN_ONLY"
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CHRS_TO_INDEX=$BASE_CHRS
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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 $?
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fi
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}
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BOWTIE_BUILD_EXE=./bowtie2-build
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if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
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if ! which bowtie2-build ; then
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echo "Could not find bowtie2-build in current directory or in PATH"
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exit 1
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else
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BOWTIE_BUILD_EXE=`which bowtie2-build`
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fi
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fi
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FTP_BASE=ftp://ftp.cbcb.umd.edu/pub/data/Bos_taurus/Bos_taurus_UMD_3.0
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OUTPUT=b_taurus
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INPUTS=
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for c in $CHRS_TO_INDEX ; do
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if [ ! -f ${c}.fa ] ; then
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F=${c}.fa.gz
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get ${FTP_BASE}/$F || (echo "Error getting $F" && exit 1)
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gunzip $F || (echo "Error unzipping $F" && exit 1)
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fi
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[ -n "$INPUTS" ] && INPUTS=$INPUTS,${c}.fa
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[ -z "$INPUTS" ] && INPUTS=${c}.fa
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done
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CMD="$BOWTIE_BUILD_EXE $* $INPUTS $OUTPUT"
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echo $CMD
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if $CMD ; then
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echo "$OUTPUT 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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