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#!/bin/bash
mkdir travis_builds
cd travis_builds
# samtools
git clone https://github.com/samtools/samtools.git
cd samtools
git checkout tags/0.1.18
perl -p -i -e 's/^(CFLAGS=\s+)[^\n]*/$1-g -Wall -O2 -fPIC #-m64 #-arch ppc/' Makefile
make 2>&1 | tail -n 1
cd ..
# push Bio-Root to front
git clone https://github.com/bioperl/Bio-Root.git
export PERL5LIB=$( pwd )/Bio-Root/lib:$( pwd ):$PERL5LIB
export SAMTOOLS=$( pwd )/samtools
echo "Bio::DB::Sam installation"
cpanm Bio::DB::Sam 2>&1 | tail -n 10
exit 0
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