4 # Downloads the sequence for a strain of e. coli from NCBI and builds a
8 GENOMES_MIRROR=ftp://ftp.ncbi.nlm.nih.gov/genomes
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 NC_008253.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}/Bacteria/Escherichia_coli_536/NC_008253.fna -o NC_008253.fna
31 wget ${GENOMES_MIRROR}/Bacteria/Escherichia_coli_536/NC_008253.fna
35 if [ ! -f NC_008253.fna ] ; then
36 echo "Could not find NC_008253.fna file!"
40 CMD="${BOWTIE_BUILD_EXE} $* -t 8 NC_008253.fna e_coli"
43 echo "e_coli index built; you may remove fasta files"
45 echo "Index building failed; see error message"