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require 'formula'
class Cufflinks < Formula
homepage 'http://cufflinks.cbcb.umd.edu/'
url 'http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.0.2.tar.gz'
sha1 '91954b4945c49ca133b39bffadf51bdf9ec2ff26'
depends_on 'boost' => :build
depends_on 'samtools' => :build
depends_on 'eigen' => :build
fails_with :clang do
build 421
end
def install
ENV['EIGEN_CPPFLAGS'] = '-I'+Formula.factory('eigen').include/'eigen3'
ENV.append 'LDFLAGS', '-lboost_system-mt'
cd 'src' do
# Fixes 120 files redefining `foreach` that break building with boost
# See http://seqanswers.com/forums/showthread.php?t=16637
`for x in *.cpp *.h; do sed 's/foreach/for_each/' $x > x; mv x $x; done`
inreplace 'common.h', 'for_each.hpp', 'foreach.hpp'
end
system "./configure", "--disable-debug", "--disable-dependency-tracking",
"--prefix=#{prefix}",
"--mandir=#{man}"
system 'make'
ENV.j1
system 'make install'
end
end
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