scripts/make_c_elegans_ws200.sh

   1 #!/bin/sh
   2
   3 #
   4 # Downloads sequence and builds Bowtie index for for C. elegans
   5 # versions WS200 from wormbase.
   6 #
   7
   8 GENOMES_MIRROR=ftp://ftp.gramene.org/pub/wormbase/genomes/c_elegans/sequences/dna
   9
  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"
  14                 exit 1
  15         else
  16                 BOWTIE_BUILD_EXE=`which bowtie-build`
  17         fi
  18 fi
  19
  20 get() {
  21         file=$1
  22         if ! wget --version >/dev/null 2>/dev/null ; then
  23                 if ! curl --version >/dev/null 2>/dev/null ; then
  24                         echo "Please install wget or curl somewhere in your PATH"
  25                         exit 1
  26                 fi
  27                 curl -o `basename $1` $1
  28                 return $?
  29         else
  30                 wget $1
  31                 return $?
  32         fi
  33 }
  34
  35 F=c_elegans.WS200.dna.fa
  36 if [ ! -f $F ] ; then
  37         FGZ=c_elegans.WS200.dna.fa.gz
  38         wget ${GENOMES_MIRROR}/$FGZ || (echo "Error getting $F" && exit 1)
  39         gunzip $FGZ || (echo "Error unzipping $F" && exit 1)
  40 fi
  41
  42 CMD="${BOWTIE_BUILD_EXE} $* $F c_elegans_ws200"
  43 echo "Running $CMD"
  44 if $CMD ; then
  45         echo "c_elegans_ws200 index built; you may remove fasta files"
  46 else
  47         echo "Index building failed; see error message"
  48 fi