43 lines
940 B
Bash
43 lines
940 B
Bash
#!/bin/sh
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SC3_BASE=ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/bigZips
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F=chromFa.tar.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 ${SC3_BASE}/$F || (echo "Error getting $F" && exit 1)
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tar xvzfO $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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