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#!/bin/sh
#
# Downloads sequence and builds Bowtie index for for C. elegans
# versions WS200 from wormbase.
#
GENOMES_MIRROR=ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/sequence/genomic
BOWTIE_BUILD_EXE=./bowtie2-build
if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
if ! which bowtie2-build ; then
echo "Could not find bowtie2-build in current directory or in PATH"
exit 1
else
BOWTIE_BUILD_EXE=`which bowtie2-build`
fi
fi
get() {
file=$1
if ! wget --version >/dev/null 2>/dev/null ; then
if ! curl --version >/dev/null 2>/dev/null ; then
echo "Please install wget or curl somewhere in your PATH"
exit 1
fi
curl -o `basename $1` $1
return $?
else
wget $1
return $?
fi
}
F=c_elegans.WS235.genomic.fa
if [ ! -f $F ] ; then
FGZ=$F.gz
wget ${GENOMES_MIRROR}/$FGZ || (echo "Error getting $F" && exit 1)
gunzip $FGZ || (echo "Error unzipping $F" && exit 1)
fi
CMD="${BOWTIE_BUILD_EXE} $* $F c_elegans_ws235"
echo "Running $CMD"
if $CMD ; then
echo "c_elegans_ws235 index built; you may remove fasta files"
else
echo "Index building failed; see error message"
fi
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