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#!/bin/sh
#
# Downloads sequence for a S. cerevisiae from CYGD. This script
# was used to build the Bowtie index for S. cerevisiae.
#
GENOMES_MIRROR=ftp://ftpmips.gsf.de/yeast/sequences
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
if [ ! -f Scerevisiae_chr.fna ] ; then
if ! which wget > /dev/null ; then
echo wget not found, looking for curl...
if ! which curl > /dev/null ; then
echo curl not found either, aborting...
else
# Use curl
curl ${GENOMES_MIRROR}/Scerevisiae_chr -o Scerevisiae_chr.fna
fi
else
# Use wget
wget ${GENOMES_MIRROR}/Scerevisiae_chr
mv Scerevisiae_chr Scerevisiae_chr.fna
fi
fi
if [ ! -f Scerevisiae_chr.fna ] ; then
echo "Could not find Scerevisiae_chr.fna file!"
exit 2
fi
CMD="$BOWTIE_BUILD_EXE $* Scerevisiae_chr.fna s_cerevisiae"
echo $CMD
if $CMD ; then
echo "s_cerevisiae index built; you may remove fasta files"
else
echo "Index building failed; see error message"
fi
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