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amos.rb
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amos.rb
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class Amos < Formula
desc "A Modular Open-Source Assembler"
homepage "http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS"
# doi "10.1002/0471250953.bi1108s33"
# tag "bioinformatics"
url "https://downloads.sourceforge.net/project/amos/amos/3.1.0/amos-3.1.0.tar.gz"
sha1 "28e799e37713594ba7147d300ecae6574beb14a4"
depends_on "blat" => :optional # for minimus2-blat
depends_on "boost" => :recommended # for Bambus 2
depends_on "mummer" => :recommended # for minimus2
depends_on "qt" => [:optional, "with-qt3support"] # for AMOS GUIs
depends_on "Statistics::Descriptive" => :perl
fails_with :clang do
build 600
cause "error: reference to 'hash' is ambiguous"
end
def install
# http://seqanswers.com/forums/showthread.php?t=17802
inreplace "src/Align/find-tandem.cc", "#include <sys/time.h>", "#include <sys/time.h>\n#include <getopt.h>"
ENV.deparallelize
args = %W[--prefix=#{prefix} --disable-dependency-tracking]
args << "--with-Boost-dir=#{Formula["boost"].opt_prefix}" if build.with? "boost"
args << "BLAT=#{Formula["blat"].opt_bin}/blat" if build.with? "blat"
if build.with? "qt"
args << "--with-qmake-qt4=#{Formula["qt"].opt_bin}/qmake"
else
args << "BUILD_QT4=no"
end
if build.with? "mummer"
args << "DELTAFILTER=#{Formula["mummer"].opt_libexec}/delta-filter"
args << "SHOWCOORDS=#{Formula["mummer"].opt_libexec}/show-coords"
end
system "./configure", *args
system "make", "install"
end
def caveats; <<-EOS.undent
The Perl modules have been installed in
#{lib}/AMOS
#{lib}/TIGR
EOS
end
test do
system "#{bin}/bank-transact", "-h"
end
end