4 # Downloads sequence for a S. cerevisiae from CYGD. This script
5 # was used to build the Bowtie index for S. cerevisiae.
8 GENOMES_MIRROR=ftp://ftpmips.gsf.de/yeast/sequences
10 BOWTIE_BUILD_EXE=./bowtie-build
11 if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
12 if ! which bowtie-build ; then
13 echo "Could not find bowtie-build in current directory or in PATH"
16 BOWTIE_BUILD_EXE=`which bowtie-build`
20 if [ ! -f Scerevisiae_chr.fna ] ; then
21 if ! which wget > /dev/null ; then
22 echo wget not found, looking for curl...
23 if ! which curl > /dev/null ; then
24 echo curl not found either, aborting...
27 curl ${GENOMES_MIRROR}/Scerevisiae_chr -o Scerevisiae_chr.fna
31 wget ${GENOMES_MIRROR}/Scerevisiae_chr
32 mv Scerevisiae_chr Scerevisiae_chr.fna
36 if [ ! -f Scerevisiae_chr.fna ] ; then
37 echo "Could not find Scerevisiae_chr.fna file!"
41 CMD="$BOWTIE_BUILD_EXE $* Scerevisiae_chr.fna s_cerevisiae"
44 echo "s_cerevisiae index built; you may remove fasta files"
46 echo "Index building failed; see error message"