4 # Downloads sequence for a D. melanogaster from flybase. Currently set
5 # to download 5.22, but F, REL, and IDX_NAME can be edited to reflect a
6 # different version number. (But note that you will usually also have
7 # to change the date in REL.)
10 GENOMES_MIRROR=ftp://ftp.flybase.net/genomes/Drosophila_melanogaster
11 F=dmel-all-chromosome-r5.22.fasta
12 REL=dmel_r5.22_FB2009_09
13 IDX_NAME=d_melanogaster_fb5_22
17 if ! wget --version >/dev/null 2>/dev/null ; then
18 if ! curl --version >/dev/null 2>/dev/null ; then
19 echo "Please install wget or curl somewhere in your PATH"
22 curl -o `basename $1` $1
25 wget -O `basename $1` $1
30 BOWTIE_BUILD_EXE=./bowtie-build
31 if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
32 if ! which bowtie-build ; then
33 echo "Could not find bowtie-build in current directory or in PATH"
36 BOWTIE_BUILD_EXE=`which bowtie-build`
42 get ${GENOMES_MIRROR}/$REL/fasta/$FGZ || (echo "Error getting $FGZ" && exit 1)
43 gunzip $FGZ || (echo "Error unzipping $FGZ" && exit 1)
46 CMD="${BOWTIE_BUILD_EXE} $* $F $IDX_NAME"
49 echo "$IDX_NAME index built; you may remove fasta files"
51 echo "Index building failed; see error message"