85 lines
2.6 KiB
Ruby
85 lines
2.6 KiB
Ruby
require 'formula'
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class Tophat < Formula
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homepage 'http://tophat.cbcb.umd.edu/'
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url 'http://tophat.cbcb.umd.edu/downloads/tophat-2.0.6.tar.gz'
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sha1 'd1c19cdccb5ddf74b8cb604a0ed1e5d33a25aae9'
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depends_on 'samtools'
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depends_on 'boost'
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# Variable length arrays using non-POD element types. Initialize with length=1
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# Reported upstream via email to tophat-cufflinks@gmail.com on 28OCT2012
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def patches; DATA; end
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def install
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# This can only build serially, otherwise it errors with no make target.
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ENV.deparallelize
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# Must add this to fix missing boost symbols. Autoconf doesn't include it.
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ENV.append 'LDFLAGS', '-lboost_system-mt'
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system "./configure", "--disable-dependency-tracking",
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"--prefix=#{prefix}"
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system "make install"
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end
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end
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__END__
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--- a/src/segment_juncs.cpp 2012-10-17 09:29:03.000000000 -0700
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+++ b/src/segment_juncs.cpp 2012-10-27 22:24:44.000000000 -0700
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@@ -4854,15 +4854,15 @@
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exit(0);
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}
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- std::set<Junction, skip_count_lt> vseg_juncs[num_threads];
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+ std::set<Junction, skip_count_lt> vseg_juncs[1];
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std::set<Junction, skip_count_lt> cov_juncs;
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std::set<Junction, skip_count_lt> butterfly_juncs;
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std::set<Junction> juncs;
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- std::set<Deletion> vdeletions[num_threads];
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- std::set<Insertion> vinsertions[num_threads];
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- FusionSimpleSet vfusions[num_threads];
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+ std::set<Deletion> vdeletions[1];
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+ std::set<Insertion> vinsertions[1];
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+ FusionSimpleSet vfusions[1];
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RefSequenceTable rt(sam_header, true);
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--- a/src/tophat_reports.cpp 2012-10-18 10:43:09.000000000 -0700
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+++ b/src/tophat_reports.cpp 2012-10-27 22:39:31.000000000 -0700
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@@ -2290,11 +2290,11 @@
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num_threads = 1;
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}
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- JunctionSet vjunctions[num_threads];
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- InsertionSet vinsertions[num_threads];
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- DeletionSet vdeletions[num_threads];
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- FusionSet vfusions[num_threads];
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- Coverage vcoverages[num_threads];
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+ JunctionSet vjunctions[1];
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+ InsertionSet vinsertions[1];
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+ DeletionSet vdeletions[1];
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+ FusionSet vfusions[1];
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+ Coverage vcoverages[1];
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vector<boost::thread*> threads;
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for (int i = 0; i < num_threads; ++i)
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@@ -2420,10 +2420,10 @@
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fprintf(stderr, "Warning: %lu small overhang junctions!\n", (long unsigned int)small_overhangs);
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*/
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- JunctionSet vfinal_junctions[num_threads];
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- InsertionSet vfinal_insertions[num_threads];
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- DeletionSet vfinal_deletions[num_threads];
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- FusionSet vfinal_fusions[num_threads];
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+ JunctionSet vfinal_junctions[1];
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+ InsertionSet vfinal_insertions[1];
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+ DeletionSet vfinal_deletions[1];
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+ FusionSet vfinal_fusions[1];
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for (int i = 0; i < num_threads; ++i)
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{
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