travis_scripts/dependency_installs

   1 #!/bin/bash
   2
   3 mkdir travis_builds
   4
   5 cd travis_builds
   6
   7 # samtools
   8 git clone https://github.com/samtools/samtools.git
   9 cd samtools
  10 git checkout tags/0.1.18
  11 perl -p -i -e 's/^(CFLAGS=\s+)[^\n]*/$1-g -Wall -O2 -fPIC #-m64 #-arch ppc/' Makefile
  12 make 2>&1 | tail -n 1
  13 cd ..
  14
  15 # push Bio-Root to front
  16 git clone https://github.com/bioperl/Bio-Root.git
  17 export PERL5LIB=$( pwd )/Bio-Root/lib:$( pwd ):$PERL5LIB
  18
  19 export SAMTOOLS=$( pwd )/samtools
  20
  21 echo "Bio::DB::Sam installation"
  22 cpanm Bio::DB::Sam 2>&1 | tail -n 10
  23
  24 exit 0