Remove formulae moved to Homebrew-science

Closes #16143.

31 files changed, 0 insertions, 957 deletions

diff --git a/Library/Aliases/fsa b/Library/Aliases/fsa
deleted file mode 120000
index 49ecb5b3b..000000000
--- a/Library/Aliases/fsa
+++ /dev/null
@@ -1 +0,0 @@
-../Formula/fast-statistical-alignment.rb
\ No newline at end of file
diff --git a/Library/Formula/abyss.rb b/Library/Formula/abyss.rb
deleted file mode 100644
index b94a0ae0e..000000000
--- a/Library/Formula/abyss.rb
+++ /dev/null
@@ -1,50 +0,0 @@
-require 'formula'
-
-class Abyss < Formula
-  homepage 'http://www.bcgsc.ca/platform/bioinfo/software/abyss'
-  url 'http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz'
-  sha1 '763dc423054421829011844ceaa5e18dc43f1ca9'
-  head 'https://github.com/sjackman/abyss.git'
-
-  # Only header files are used from these packages, so :build is appropriate
-  depends_on 'boost149' => :build
-  depends_on 'google-sparsehash' => :build
-
-  # Snow Leopard comes with mpi but Lion does not
-  depends_on 'open-mpi' if MacOS.version >= :lion
-
-  # strip breaks the ability to read compressed files.
-  skip_clean 'bin'
-
-  # Fix a compiler error on OS X 10.8 Mountain Lion.
-  # This issue is fixed upstream:
-  # https://github.com/sjackman/abyss/issues/13
-  def patches
-    DATA
-  end
-
-  def install
-    system "./configure", "--disable-dependency-tracking",
-                          "--prefix=#{prefix}"
-    system "make install"
-  end
-
-  def test
-    system "#{bin}/ABYSS", "--version"
-  end
-end
-
-__END__
-diff --git a/Graph/ContigGraphAlgorithms.h b/Graph/ContigGraphAlgorithms.h
-index 023a898..0eac936 100644
---- a/Graph/ContigGraphAlgorithms.h
-+++ b/Graph/ContigGraphAlgorithms.h
-@@ -329,7 +329,7 @@ size_t addComplementaryEdges(ContigGraph<DG>& g)
-		if (!found) {
-			add_edge(vc, uc, g[e], static_cast<DG&>(g));
-			numAdded++;
--		} else if (g[e] != g[f]) {
-+		} else if (!(g[e] == g[f])) {
-			// The edge properties do not agree. Select the better.
-			g[e] = g[f] = BetterDistanceEst()(g[e], g[f]);
-		}
diff --git a/Library/Formula/arow++.rb b/Library/Formula/arow++.rb
deleted file mode 100644
index 3860d75ac..000000000
--- a/Library/Formula/arow++.rb
+++ /dev/null
@@ -1,12 +0,0 @@
-require 'formula'
-
-class Arowxx < Formula
-  homepage 'http://code.google.com/p/arowpp/'
-  url 'http://arowpp.googlecode.com/files/AROW%2B%2B-0.1.2.tar.gz'
-  sha1 '82d3a25ea30db1b3b412a0ba723f6196ebb69d52'
-
-  def install
-    system "./configure", "--prefix=#{prefix}"
-    system "make install"
-  end
-end
diff --git a/Library/Formula/bamtools.rb b/Library/Formula/bamtools.rb
deleted file mode 100644
index 4acf8e59c..000000000
--- a/Library/Formula/bamtools.rb
+++ /dev/null
@@ -1,70 +0,0 @@
-require 'formula'
-
-class Bamtools < Formula
-  homepage 'https://github.com/pezmaster31/bamtools'
-  url 'https://github.com/downloads/pezmaster31/bamtools/bamtools-1.0.2.tar.gz'
-  sha1 '70d4a1f8d7da73dd381b609b618ed19b6184366e'
-
-  head 'https://github.com/pezmaster31/bamtools.git'
-
-  depends_on 'cmake' => :build
-
-  # Install libbamtools in /usr/local/lib.
-  # Link statically with libbamtools-util and libjsoncpp, since
-  # they're not installed by default. Sent upstream:
-  # https://github.com/pezmaster31/bamtools/pull/55
-  def patches
-    DATA
-  end
-
-  def install
-    mkdir 'default' do
-      system "cmake", "..", *std_cmake_args
-      system "make install"
-    end
-  end
-
-  def test
-    system "#{bin}/bamtools", "--version"
-  end
-end
-
-__END__
-diff -ur bamtools-1.0.2.orig/src/api/CMakeLists.txt bamtools-1.0.2/src/api/CMakeLists.txt
---- bamtools-1.0.2.orig/src/api/CMakeLists.txt	2011-09-09 18:59:44.000000000 -0700
-+++ bamtools-1.0.2/src/api/CMakeLists.txt	2012-06-15 10:46:18.000000000 -0700
-@@ -54,8 +54,8 @@
- target_link_libraries( BamTools-static z )
- 
- # set library install destinations
--install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin")
--install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools")
-+install( TARGETS BamTools LIBRARY DESTINATION "lib" RUNTIME DESTINATION "bin")
-+install( TARGETS BamTools-static ARCHIVE DESTINATION "lib")
- 
- # export API headers
- include(../ExportHeader.cmake)
-diff -ur bamtools-1.0.2.orig/src/third_party/jsoncpp/CMakeLists.txt bamtools-1.0.2/src/third_party/jsoncpp/CMakeLists.txt
---- bamtools-1.0.2.orig/src/third_party/jsoncpp/CMakeLists.txt	2012-06-15 10:39:40.000000000 -0700
-+++ bamtools-1.0.2/src/third_party/jsoncpp/CMakeLists.txt	2012-06-15 10:41:49.000000000 -0700
-@@ -10,7 +10,7 @@
- add_definitions( -fPIC ) # (attempt to force PIC compiling on CentOS, not being set on shared libs by CMake)
- 
- # create jsoncpp library
--add_library ( jsoncpp SHARED 
-+add_library ( jsoncpp STATIC 
-               json_reader.cpp
-               json_value.cpp
-               json_writer.cpp
-diff -ur bamtools-1.0.2.orig/src/utils/CMakeLists.txt bamtools-1.0.2/src/utils/CMakeLists.txt
---- bamtools-1.0.2.orig/src/utils/CMakeLists.txt	2012-06-15 10:39:40.000000000 -0700
-+++ bamtools-1.0.2/src/utils/CMakeLists.txt	2012-06-15 10:41:34.000000000 -0700
-@@ -13,7 +13,7 @@
- add_definitions( -fPIC ) # (attempt to force PIC compiling on CentOS, not being set on shared libs by CMake)
- 
- # create BamTools utils library
--add_library ( BamTools-utils SHARED 
-+add_library ( BamTools-utils STATIC 
-               bamtools_fasta.cpp
-               bamtools_options.cpp
-               bamtools_pileup_engine.cpp
diff --git a/Library/Formula/blast.rb b/Library/Formula/blast.rb
deleted file mode 100644
index 99edc4c3f..000000000
--- a/Library/Formula/blast.rb
+++ /dev/null
@@ -1,39 +0,0 @@
-require 'formula'
-
-class Blast < Formula
-  homepage 'http://blast.ncbi.nlm.nih.gov/'
-  url 'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.27/ncbi-blast-2.2.27+-src.tar.gz'
-  version '2.2.27'
-  sha1 '51529c9fada67e890b994213d26f4177fa3d23d8'
-
-  fails_with :llvm do
-    build 5658
-    cause <<-EOS.undent
-      Compiler segfaults.
-    EOS
-  end
-
-  option 'with-dll', "Create dynamic binaries instead of static"
-
-  def install
-    args = ["--prefix=#{prefix}"]
-    args << "--with-dll" if build.include? 'with-dll'
-
-    cd 'c++' do
-      system "./configure", *args
-      system "make"
-      system "make install"
-    end
-  end
-
-  def caveats; <<-EOS.undent
-    Using the option '--with-dll' will create dynamic binaries instead of
-    static. NCBI Blast static binaries are approximately 28-times larger
-    than dynamic binaries.
-
-    Static binaries should be used for speed if the executable requires
-    fast startup time, such as if another program is frequently restarting
-    the blast executables.
-    EOS
-  end
-end
diff --git a/Library/Formula/bowtie.rb b/Library/Formula/bowtie.rb
deleted file mode 100644
index b6b95cd08..000000000
--- a/Library/Formula/bowtie.rb
+++ /dev/null
@@ -1,12 +0,0 @@
-require 'formula'
-
-class Bowtie < Formula
-  homepage 'http://bowtie-bio.sourceforge.net/index.shtml'
-  url 'http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-src.zip'
-  sha1 '56fd4dfd1d8ef995f041d11ce6078dd1e22a655f'
-
-  def install
-    system "make"
-    bin.install %W(bowtie bowtie-build bowtie-inspect)
-  end
-end
diff --git a/Library/Formula/bwa.rb b/Library/Formula/bwa.rb
deleted file mode 100644
index 5a66b4641..000000000
--- a/Library/Formula/bwa.rb
+++ /dev/null
@@ -1,84 +0,0 @@
-require 'formula'
-
-class Bwa < Formula
-  homepage 'http://bio-bwa.sourceforge.net/'
-  url 'http://downloads.sourceforge.net/project/bio-bwa/bwa-0.6.2.tar.bz2'
-  sha1 'fd3d0666a89d189b642d6f1c4cfa9c29123c12bc'
-
-  head 'https://github.com/lh3/bwa.git'
-
-  # These inline functions cause undefined symbol errors with CLANG.
-  # Fixed upstream for next release. See:
-  # https://github.com/lh3/bwa/pull/11
-  def patches; DATA; end
-
-  def install
-    system "make", "CC=#{ENV.cc}", "CFLAGS=#{ENV.cflags}"
-    bin.install "bwa"
-    man1.install "bwa.1"
-  end
-end
-
-__END__
-diff --git a/bwt.c b/bwt.c
-index fcc141e..966b718 100644
---- a/bwt.c
-+++ b/bwt.c
-@@ -95,7 +95,7 @@ static inline int __occ_aux(uint64_t y, int c)
-	return ((y + (y >> 4)) & 0xf0f0f0f0f0f0f0full) * 0x101010101010101ull >> 56;
- }
-
--inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c)
-+bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c)
- {
-	bwtint_t n, l, j;
-	uint32_t *p;
-@@ -121,7 +121,7 @@ inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c)
- }
-
- // an analogy to bwt_occ() but more efficient, requiring k <= l
--inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol)
-+void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol)
- {
-	bwtint_t _k, _l;
-	_k = (k >= bwt->primary)? k-1 : k;
-@@ -158,7 +158,7 @@ inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint
-	((bwt)->cnt_table[(b)&0xff] + (bwt)->cnt_table[(b)>>8&0xff]		\
-	 + (bwt)->cnt_table[(b)>>16&0xff] + (bwt)->cnt_table[(b)>>24])
-
--inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
-+void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
- {
-	bwtint_t l, j, x;
-	uint32_t *p;
-@@ -178,7 +178,7 @@ inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
- }
-
- // an analogy to bwt_occ4() but more efficient, requiring k <= l
--inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4])
-+void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4])
- {
-	bwtint_t _k, _l;
-	_k = (k >= bwt->primary)? k-1 : k;
-diff --git a/bwt_lite.c b/bwt_lite.c
-index dd411e1..902e0fc 100644
---- a/bwt_lite.c
-+++ b/bwt_lite.c
-@@ -65,7 +65,7 @@ inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c)
-	if (c == 0) n -= 15 - (k&15); // corrected for the masked bits
-	return n;
- }
--inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4])
-+void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4])
- {
-	uint32_t x, b;
-	if (k == (uint32_t)(-1)) {
-@@ -80,7 +80,7 @@ inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4])
-	x -= 15 - (k&15);
-	cnt[0] += x&0xff; cnt[1] += x>>8&0xff; cnt[2] += x>>16&0xff; cnt[3] += x>>24;
- }
--inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4])
-+void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4])
- {
-	bwtl_occ4(bwt, k, cntk);
-	bwtl_occ4(bwt, l, cntl);
diff --git a/Library/Formula/cd-hit.rb b/Library/Formula/cd-hit.rb
deleted file mode 100644
index cc5eafec0..000000000
--- a/Library/Formula/cd-hit.rb
+++ /dev/null
@@ -1,14 +0,0 @@
-require 'formula'
-
-class CdHit < Formula
-  homepage 'http://bioinformatics.org/cd-hit/'
-  url 'http://www.bioinformatics.org/downloads/index.php/cd-hit/cd-hit-v4.5.4-2011-03-07.tgz'
-  version '4.5.4'
-  sha1 '743c4b6ec79b9d5acd1e1171587e96c03e3e3003'
-
-  def install
-    system "make"
-    bin.mkpath
-    system "make", "PREFIX=#{bin}", "install"
-  end
-end
diff --git a/Library/Formula/clustal-omega.rb b/Library/Formula/clustal-omega.rb
deleted file mode 100644
index 535665900..000000000
--- a/Library/Formula/clustal-omega.rb
+++ /dev/null
@@ -1,15 +0,0 @@
-require 'formula'
-
-class ClustalOmega < Formula
-  homepage 'http://www.clustal.org/omega/'
-  url 'http://www.clustal.org/omega/clustal-omega-1.1.0.tar.gz'
-  sha1 'b8c8ac500811c50a335c9dc2fcaf47a7245fa6a0'
-
-  depends_on 'argtable'
-
-  def install
-    system "./configure", "--disable-debug", "--disable-dependency-tracking",
-                          "--prefix=#{prefix}"
-    system "make install"
-  end
-end
diff --git a/Library/Formula/clustal-w.rb b/Library/Formula/clustal-w.rb
deleted file mode 100644
index 7fe54065d..000000000
--- a/Library/Formula/clustal-w.rb
+++ /dev/null
@@ -1,12 +0,0 @@
-require 'formula'
-
-class ClustalW < Formula
-  homepage 'http://www.clustal.org/clustal2/'
-  url 'http://www.clustal.org/download/2.1/clustalw-2.1.tar.gz'
-  sha1 'f29784f68585544baa77cbeca6392e533d4cf433'
-
-  def install
-    system "./configure", "--disable-dependency-tracking", "--prefix=#{prefix}"
-    system "make install"
-  end
-end
diff --git a/Library/Formula/cufflinks.rb b/Library/Formula/cufflinks.rb
deleted file mode 100644
index 5bdd63500..000000000
--- a/Library/Formula/cufflinks.rb
+++ /dev/null
@@ -1,32 +0,0 @@
-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
diff --git a/Library/Formula/dadadodo.rb b/Library/Formula/dadadodo.rb
deleted file mode 100644
index a1a916ee7..000000000
--- a/Library/Formula/dadadodo.rb
+++ /dev/null
@@ -1,12 +0,0 @@
-require 'formula'
-
-class Dadadodo < Formula
-  homepage 'http://www.jwz.org/dadadodo/'
-  url 'http://www.jwz.org/dadadodo/dadadodo-1.04.tar.gz'
-  sha1 '20b3c802db70c8c4fddf751e668aa6218c085643'
-
-  def install
-    system "make", "CC=#{ENV.cc}", "CFLAGS=#{ENV.cflags}", "LDFLAGS=#{ENV.ldflags}"
-    bin.install "dadadodo"
-  end
-end
diff --git a/Library/Formula/emboss.rb b/Library/Formula/emboss.rb
deleted file mode 100644
index e3ee18ab8..000000000
--- a/Library/Formula/emboss.rb
+++ /dev/null
@@ -1,28 +0,0 @@
-require 'formula'
-
-class Emboss < Formula
-  homepage 'http://emboss.sourceforge.net/'
-  url 'ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.5.7.tar.gz'
-  sha1 '907231eafe07917ae0bf9c5da2e7cdc3e9bae03a'
-
-  option 'without-x', 'Build without X11 support'
-
-  depends_on 'pkg-config' => :build
-  depends_on 'libharu'    => :optional
-  depends_on 'gd'         => :optional
-  depends_on :libpng      => :recommended
-  depends_on :x11 unless build.include? 'without-x'
-
-  def install
-    args = %W[
-      --disable-debug
-      --disable-dependency-tracking
-      --prefix=#{prefix}
-      --enable-64
-      --with-thread
-    ]
-    args << '--without-x' if build.include? 'without-x'
-    system './configure', *args
-    system 'make install'
-  end
-end
diff --git a/Library/Formula/fast-statistical-alignment.rb b/Library/Formula/fast-statistical-alignment.rb
deleted file mode 100644
index f3ea4338d..000000000
--- a/Library/Formula/fast-statistical-alignment.rb
+++ /dev/null
@@ -1,23 +0,0 @@
-require 'formula'
-
-class FastStatisticalAlignment < Formula
-  homepage 'http://fsa.sourceforge.net/'
-  url 'http://downloads.sourceforge.net/project/fsa/fsa-1.15.7.tar.gz'
-  sha1 '322c8270d027b573b0781d8729f0917206e9d775'
-
-  fails_with :clang do
-    build 412
-    cause <<-EOS.undent
-      In file included from ../../src/annealing/dotplot.h:14:
-      ../../src/util/array2d.h:258:82: error: member reference base type 'array2d_type *const' (aka 'array2d<value_type, xy_container_type> *const') is not a
-            structure or union
-            Column_iterator end() const { return Column_iterator (_array, _col, _array.rows()); }
-      EOS
-  end
-
-  def install
-    system "./configure", "--disable-debug", "--disable-dependency-tracking",
-                          "--prefix=#{prefix}"
-    system "make install"
-  end
-end
diff --git a/Library/Formula/fastx_toolkit.rb b/Library/Formula/fastx_toolkit.rb
deleted file mode 100644
index 418e36cf5..000000000
--- a/Library/Formula/fastx_toolkit.rb
+++ /dev/null
@@ -1,32 +0,0 @@
-require 'formula'
-
-class FastxToolkit < Formula
-  homepage 'http://hannonlab.cshl.edu/fastx_toolkit/'
-  url 'http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit-0.0.13.2.tar.bz2'
-  sha1 '51fd9ddc1fc1ffea29d7cabc02e46dd8a1b860ec'
-
-  depends_on 'pkg-config' => :build
-  depends_on 'libgtextutils'
-
-  def install
-    system "./configure", "--disable-debug",
-                          "--disable-dependency-tracking",
-                          "--prefix=#{prefix}"
-    system "make install"
-  end
-
-  def test
-    fixture = <<-EOS.undent
-      >MY-ID
-      AAAAAGGGGG
-      CCCCCTTTTT
-      AGCTN
-      EOS
-    expect = <<-EOS.undent
-      >MY-ID
-      AAAAAGGGGGCCCCCTTTTTAGCTN
-      EOS
-    actual = `echo "#{fixture}" | #{bin}/fasta_formatter`
-    actual == expect
-  end
-end
diff --git a/Library/Formula/gmap-gsnap.rb b/Library/Formula/gmap-gsnap.rb
deleted file mode 100644
index 1e7a1b5af..000000000
--- a/Library/Formula/gmap-gsnap.rb
+++ /dev/null
@@ -1,31 +0,0 @@
-require 'formula'
-
-class GmapGsnap < Formula
-  homepage 'http://research-pub.gene.com/gmap'
-  url 'http://research-pub.gene.com/gmap/src/gmap-gsnap-2012-07-20.tar.gz'
-  sha1 '9edb7750b923842f9c877f59934cdfd9f5cdf2b7'
-  version "2012-07-20"
-
-  depends_on "samtools"
-
-  def install
-    ENV['CC'] = "#{ENV.cc} -O3 -m#{MacOS.prefer_64_bit? ? 64 : 32}"
-    system "./configure", "--prefix=#{prefix}"
-    system "make"
-    system "make install"
-  end
-
-  def caveats; <<-EOF.undent
-    You will need to either download or build indexed search databases.
-    See the readme file for how to do this:
-      http://research-pub.gene.com/gmap/src/README
-
-    Databases will be installed to:
-      #{share}
-    EOF
-  end
-
-  def test
-    system "#{bin}/gsnap", "--version"
-  end
-end
diff --git a/Library/Formula/hmmer.rb b/Library/Formula/hmmer.rb
deleted file mode 100644
index 71468ad56..000000000
--- a/Library/Formula/hmmer.rb
+++ /dev/null
@@ -1,23 +0,0 @@
-require 'formula'
-
-class Hmmer < Formula
-  homepage 'http://hmmer.janelia.org/'
-  url 'http://selab.janelia.org/software/hmmer3/3.0/hmmer-3.0.tar.gz'
-  sha1 '77803c0bdb3ab07b7051a4c68c0564de31940c6d'
-
-  def install
-    system "./configure", "--prefix=#{prefix}"
-    system "make install"
-
-    # Install man pages manually as long as automatic man page install
-    # is deactivated in the HMMER makefile. If this changes in future
-    # versions of HMMER, these lines can be removed.
-
-    cd "documentation/man" do
-      # rename all *.man files to *.1 and install them into man1 section
-      Dir["*.man"].each do |f|
-        man1.install f => f.sub(/\.man/, ".1")
-      end
-    end
-  end
-end
diff --git a/Library/Formula/mira.rb b/Library/Formula/mira.rb
deleted file mode 100644
index e51dd647d..000000000
--- a/Library/Formula/mira.rb
+++ /dev/null
@@ -1,129 +0,0 @@
-require 'formula'
-
-class Mira < Formula
-  homepage 'http://sourceforge.net/apps/mediawiki/mira-assembler/'
-  url 'http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-3.4.0.2.tar.bz2'
-  sha1 'bf40ce540cdd794d0a1653b5fb829ab2b0829198'
-
-
-  depends_on 'boost'
-  depends_on 'google-perftools'
-  depends_on 'docbook'
-
-  # Fix a compiler error on OS X 10.8
-  # http://www.freelists.org/post/mira_talk/Type-mismatch-of-LexerInput-and-LexerOutput-PATCH
-  def patches
-    DATA if MacOS.version >= :mountain_lion
-  end
-
-  def install
-    system "./configure", "--disable-debug",
-                          "--disable-dependency-tracking",
-                          "--prefix=#{prefix}"
-    # Link with boost_system for boost::system::system_category().
-    # http://www.freelists.org/post/mira_talk/Linking-requires-boost-system
-    system "make LIBS=-lboost_system-mt install"
-  end
-
-  def test
-    system "#{bin}/mira"
-  end
-end
-
-__END__
-diff -ur a/src/EdIt/parameters_flexer.cc b/src/EdIt/parameters_flexer.cc
---- a/src/EdIt/parameters_flexer.cc	2012-08-29 10:33:02.000000000 -0700
-+++ b/src/EdIt/parameters_flexer.cc	2012-10-22 10:58:26.000000000 -0700
-@@ -1367,9 +1367,9 @@
- }
-
- #ifdef YY_INTERACTIVE
--int yyFlexLexer::LexerInput( char* buf, int /* max_size */ )
-+size_t yyFlexLexer::LexerInput( char* buf, size_t /* max_size */ )
- #else
--int yyFlexLexer::LexerInput( char* buf, int max_size )
-+size_t yyFlexLexer::LexerInput( char* buf, size_t max_size )
- #endif
- {
-	if ( yyin->eof() || yyin->fail() )
-@@ -1396,7 +1396,7 @@
- #endif
- }
-
--void yyFlexLexer::LexerOutput( const char* buf, int size )
-+void yyFlexLexer::LexerOutput( const char* buf, size_t size )
- {
-	(void) yyout->write( buf, size );
- }
-diff -ur a/src/caf/caf_flexer.cc b/src/caf/caf_flexer.cc
---- a/src/caf/caf_flexer.cc	2012-08-29 10:33:02.000000000 -0700
-+++ b/src/caf/caf_flexer.cc	2012-10-22 10:58:58.000000000 -0700
-@@ -2291,9 +2291,9 @@
- }
-
- #ifdef YY_INTERACTIVE
--int yyFlexLexer::LexerInput( char* buf, int /* max_size */ )
-+size_t yyFlexLexer::LexerInput( char* buf, size_t /* max_size */ )
- #else
--int yyFlexLexer::LexerInput( char* buf, int max_size )
-+size_t yyFlexLexer::LexerInput( char* buf, size_t max_size )
- #endif
- {
-	if ( yyin->eof() || yyin->fail() )
-@@ -2320,7 +2320,7 @@
- #endif
- }
-
--void yyFlexLexer::LexerOutput( const char* buf, int size )
-+void yyFlexLexer::LexerOutput( const char* buf, size_t size )
- {
-	(void) yyout->write( buf, size );
- }
-diff -ur a/src/io/exp_flexer.cc b/src/io/exp_flexer.cc
---- a/src/io/exp_flexer.cc	2012-08-29 10:33:01.000000000 -0700
-+++ b/src/io/exp_flexer.cc	2012-10-22 10:55:35.000000000 -0700
-@@ -1405,9 +1405,9 @@
- }
-
- #ifdef YY_INTERACTIVE
--int yyFlexLexer::LexerInput( char* buf, int /* max_size */ )
-+size_t yyFlexLexer::LexerInput( char* buf, size_t /* max_size */ )
- #else
--int yyFlexLexer::LexerInput( char* buf, int max_size )
-+size_t yyFlexLexer::LexerInput( char* buf, size_t max_size )
- #endif
- {
-	if ( yyin->eof() || yyin->fail() )
-@@ -1434,7 +1434,7 @@
- #endif
- }
-
--void yyFlexLexer::LexerOutput( const char* buf, int size )
-+void yyFlexLexer::LexerOutput( const char* buf, size_t size )
- {
-	(void) yyout->write( buf, size );
- }
-diff -ur a/src/mira/parameters_flexer.cc b/src/mira/parameters_flexer.cc
---- a/src/mira/parameters_flexer.cc	2012-08-29 10:33:02.000000000 -0700
-+++ b/src/mira/parameters_flexer.cc	2012-10-22 10:57:50.000000000 -0700
-@@ -7310,9 +7310,9 @@
- }
-
- #ifdef YY_INTERACTIVE
--int yyFlexLexer::LexerInput( char* buf, int /* max_size */ )
-+size_t yyFlexLexer::LexerInput( char* buf, size_t /* max_size */ )
- #else
--int yyFlexLexer::LexerInput( char* buf, int max_size )
-+size_t yyFlexLexer::LexerInput( char* buf, size_t max_size )
- #endif
- {
-	if ( yyin->eof() || yyin->fail() )
-@@ -7339,7 +7339,7 @@
- #endif
- }
-
--void yyFlexLexer::LexerOutput( const char* buf, int size )
-+void yyFlexLexer::LexerOutput( const char* buf, size_t size )
- {
-	(void) yyout->write( buf, size );
- }
diff --git a/Library/Formula/mrfast.rb b/Library/Formula/mrfast.rb
deleted file mode 100644
index 9582729da..000000000
--- a/Library/Formula/mrfast.rb
+++ /dev/null
@@ -1,18 +0,0 @@
-require 'formula'
-
-class Mrfast < Formula
-  homepage 'http://mrfast.sourceforge.net/'
-  url 'http://sourceforge.net/projects/mrfast/files/mrfast/mrfast-2.5.0.2.tar.gz'
-  sha1 '149d45a2ec9c5def879c20a2fac0799dc85d1606'
-
-  def install
-    system "make", "CC=#{ENV.cc}", "CFLAGS=-c #{ENV.cflags}"
-    bin.install 'mrfast'
-  end
-
-  def test
-    actual = `#{bin}/mrfast -h`.split("\n").first
-    expect = "mrFAST : Micro-Read Fast Alignment Search Tool."
-    expect.eql? actual
-  end
-end
diff --git a/Library/Formula/muscle.rb b/Library/Formula/muscle.rb
deleted file mode 100644
index c66d8306e..000000000
--- a/Library/Formula/muscle.rb
+++ /dev/null
@@ -1,37 +0,0 @@
-require 'formula'
-
-class Muscle < Formula
-  homepage 'http://www.drive5.com/muscle/'
-  url 'http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz'
-  version '3.8.31'
-  sha1 '2fe55db73ff4e7ac6d4ca692f8f213d1c5071dac'
-
-  # This patch makes 3.8.31 build on OSX >= Lion.
-  # It has been reported upstream but not fixed yet.
-  def patches
-    DATA
-  end
-
-  def install
-    cd "src" do
-      system "make"
-      bin.install "muscle"
-    end
-  end
-end
-
-__END__
---- a/src/globalsosx.cpp	2010-04-28 16:43:42.000000000 -0700
-+++ b/src/globalsosx.cpp	2012-11-20 15:53:14.000000000 -0800
-@@ -13,10 +13,10 @@
- #include <netinet/icmp6.h>

- #include <sys/vmmeter.h>

- #include <sys/proc.h>

-+#include <mach/vm_statistics.h>
- #include <mach/task_info.h>

- #include <mach/task.h>

- #include <mach/mach_init.h>

--#include <mach/vm_statistics.h>

- 

- const double DEFAULT_RAM = 1e9;

- const double DEFAULT_MEM_USE = 1e6;

diff --git a/Library/Formula/paml.rb b/Library/Formula/paml.rb
deleted file mode 100644
index 791714662..000000000
--- a/Library/Formula/paml.rb
+++ /dev/null
@@ -1,18 +0,0 @@
-require 'formula'
-
-class Paml < Formula
-  homepage 'http://abacus.gene.ucl.ac.uk/software/paml.html'
-  url 'http://abacus.gene.ucl.ac.uk/software/paml4.6.tgz'
-  sha1 '2d12d50695a0d6d324781e75594783e250fbb795'
-
-  def install
-    cd 'src' do
-      system "make", "CC=#{ENV.cc}", "CFLAGS=#{ENV.cflags}"
-      bin.install %w[baseml basemlg codeml pamp evolver yn00 chi2]
-    end
-
-    (share+'paml').install 'dat'
-    (share+'paml').install Dir['*.ctl']
-    doc.install Dir['doc/*']
-  end
-end
diff --git a/Library/Formula/phyml.rb b/Library/Formula/phyml.rb
deleted file mode 100644
index 841d0aecf..000000000
--- a/Library/Formula/phyml.rb
+++ /dev/null
@@ -1,35 +0,0 @@
-require 'formula'
-
-class Phyml < Formula
-  homepage 'http://www.atgc-montpellier.fr/phyml/'
-  url 'https://phyml.googlecode.com/files/phyml-20120412.tar.gz'
-  sha1 '8a4699ad2bba7e2f76c8eefa277d29290f92071c'
-
-  def install
-    # separate steps required
-    system "./configure", "--prefix=#{prefix}"
-    system "make"
-
-    system "./configure", "--prefix=#{prefix}", "--enable-phytime"
-    system "make"
-
-    bin.install %w(src/phyml src/phytime)
-    doc.install Dir['doc/phyml-manual.pdf']
-    rm_rf Dir['examples/.svn']
-    chmod 0644, Dir['examples/*']
-    share.install Dir['examples/*']
-  end
-
-  def caveats; <<-EOS.undent
-    Examples have been installed here:
-      #{share}
-
-    See options for phyml by running:
-      phmyl --help
-
-    PhyML must be run with the "-i" option to specify an input or it will
-    segfault. Example:
-      phyml -i #{share}/nucleic
-    EOS
-  end
-end
diff --git a/Library/Formula/plink.rb b/Library/Formula/plink.rb
deleted file mode 100644
index b9a3f09b2..000000000
--- a/Library/Formula/plink.rb
+++ /dev/null
@@ -1,15 +0,0 @@
-require 'formula'
-
-class Plink < Formula
-  url 'http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-1.07-src.zip'
-  homepage 'http://pngu.mgh.harvard.edu/~purcell/plink/'
-  sha1 'd41a2d014ebc02bf11e5235292b50fad6dedd407'
-
-  def install
-    ENV.deparallelize
-    inreplace "Makefile", "SYS = UNIX", "SYS = MAC"
-    system "make"
-    (share+'plink').install %w{test.map test.ped}
-    bin.install "plink"
-  end
-end
diff --git a/Library/Formula/primer3.rb b/Library/Formula/primer3.rb
deleted file mode 100644
index d5209328b..000000000
--- a/Library/Formula/primer3.rb
+++ /dev/null
@@ -1,14 +0,0 @@
-require 'formula'
-
-class Primer3 < Formula
-  homepage 'http://primer3.sourceforge.net/'
-  url 'https://sourceforge.net/projects/primer3/files/primer3/2.3.4/primer3-2.3.4.tar.gz'
-  sha1 '850d8e5cfbe84cdf3e4955a3974a6531a8ac6516'
-
-  def install
-    cd "src" do
-      system "make all"
-      bin.install %w(primer3_core ntdpal oligotm long_seq_tm_test)
-    end
-  end
-end
diff --git a/Library/Formula/prodigal.rb b/Library/Formula/prodigal.rb
deleted file mode 100644
index 664c59e18..000000000
--- a/Library/Formula/prodigal.rb
+++ /dev/null
@@ -1,12 +0,0 @@
-require 'formula'
-
-class Prodigal < Formula
-  homepage 'http://prodigal.ornl.gov/'
-  url 'http://prodigal.googlecode.com/files/prodigal.v2_60.tar.gz'
-  sha1 '23a45dafedd98c04f9a4edbe82b037120644eaa2'
-
-  def install
-    system "make"
-    bin.install 'prodigal'
-  end
-end
diff --git a/Library/Formula/quicktree.rb b/Library/Formula/quicktree.rb
deleted file mode 100644
index ca2f9ff4e..000000000
--- a/Library/Formula/quicktree.rb
+++ /dev/null
@@ -1,13 +0,0 @@
-require 'formula'
-
-class Quicktree < Formula
-  url 'ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz'
-  version '1.1'
-  homepage 'http://www.sanger.ac.uk/resources/software/quicktree/'
-  sha1 '9924d51801149d59fd90f704aa7e5802f7b1ef31'
-
-  def install
-    system "make"
-    bin.install "bin/quicktree"
-  end
-end
diff --git a/Library/Formula/samtools.rb b/Library/Formula/samtools.rb
deleted file mode 100644
index 4ff94e2b7..000000000
--- a/Library/Formula/samtools.rb
+++ /dev/null
@@ -1,24 +0,0 @@
-require 'formula'
-
-class Samtools < Formula
-  url 'http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2'
-  homepage 'http://samtools.sourceforge.net/'
-  sha1 '77be35df7a90c288a003ff826ba99aef53b2fbe6'
-  head 'https://samtools.svn.sourceforge.net/svnroot/samtools/trunk/samtools'
-
-  def install
-    system "make"
-    system "make razip"
-    cd 'bcftools' do
-      system "make"
-    end
-
-    bin.install %w{samtools razip bcftools/bcftools bcftools/vcfutils.pl}
-    bin.install %w{misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/seqtk misc/wgsim}
-    bin.install Dir['misc/*.pl']
-    lib.install 'libbam.a'
-    man1.install %w{samtools.1}
-    (share+'samtools').install %w{examples}
-    (include+'bam').install Dir['*.h']
-  end
-end
diff --git a/Library/Formula/sga.rb b/Library/Formula/sga.rb
deleted file mode 100644
index cb20dfa48..000000000
--- a/Library/Formula/sga.rb
+++ /dev/null
@@ -1,35 +0,0 @@
-require 'formula'
-
-class Sga < Formula
-  homepage 'https://github.com/jts/sga'
-  url 'https://github.com/jts/sga/tarball/v0.9.35'
-  sha1 'e505f46fc6ba0e991096d7d9a9d50d37c94e4d4c'
-
-  head 'https://github.com/jts/sga.git'
-
-  depends_on :autoconf => :build
-  depends_on :automake => :build
-  # Only header files are used, so :build is appropriate
-  depends_on 'google-sparsehash' => :build
-  depends_on 'bamtools'
-
-  # Fix two compiler errors. Both fixed upstream.
-  def patches
-    ['http://github.com/jts/sga/commit/b4efb323ed.diff',
-     'https://github.com/jts/sga/commit/dfe74633fb.diff'] unless build.head?
-  end
-
-  def install
-    cd 'src' do
-      system "./autogen.sh"
-      system "./configure", "--disable-debug", "--disable-dependency-tracking",
-                            "--prefix=#{prefix}",
-                            "--with-bamtools=#{HOMEBREW_PREFIX}"
-      system "make install"
-    end
-  end
-
-  def test
-    system "#{bin}/sga", "--version"
-  end
-end
diff --git a/Library/Formula/tabix.rb b/Library/Formula/tabix.rb
deleted file mode 100644
index 964b19aad..000000000
--- a/Library/Formula/tabix.rb
+++ /dev/null
@@ -1,15 +0,0 @@
-require 'formula'
-
-class Tabix < Formula
-  homepage 'http://samtools.sourceforge.net/'
-  url 'http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2'
-  sha1 '4f0cac0da585abddc222956cac1b6e508ca1c49e'
-  head 'https://samtools.svn.sourceforge.net/svnroot/samtools/trunk/tabix'
-
-  def install
-    system "make"
-    bin.install %w{tabix bgzip}
-    man1.install 'tabix.1'
-    ln_s man1+'tabix.1', man1+'bgzip.1'
-  end
-end
diff --git a/Library/Formula/tophat.rb b/Library/Formula/tophat.rb
deleted file mode 100644
index 4b2e558f8..000000000
--- a/Library/Formula/tophat.rb
+++ /dev/null
@@ -1,84 +0,0 @@
-require 'formula'
-
-class Tophat < Formula
-  homepage 'http://tophat.cbcb.umd.edu/'
-  url 'http://tophat.cbcb.umd.edu/downloads/tophat-2.0.6.tar.gz'
-  sha1 'd1c19cdccb5ddf74b8cb604a0ed1e5d33a25aae9'
-
-  depends_on 'samtools'
-  depends_on 'boost'
-
-  # Variable length arrays using non-POD element types. Initialize with length=1
-  # Reported upstream via email to tophat-cufflinks@gmail.com on 28OCT2012
-  def patches; DATA; end
-
-  def install
-    # This can only build serially, otherwise it errors with no make target.
-    ENV.deparallelize
-
-    # Must add this to fix missing boost symbols. Autoconf doesn't include it.
-    ENV.append 'LDFLAGS', '-lboost_system-mt'
-
-    system "./configure", "--disable-dependency-tracking",
-                          "--prefix=#{prefix}"
-    system "make install"
-  end
-end
-
-__END__
---- a/src/segment_juncs.cpp	2012-10-17 09:29:03.000000000 -0700
-+++ b/src/segment_juncs.cpp	2012-10-27 22:24:44.000000000 -0700
-@@ -4854,15 +4854,15 @@
-       exit(0);
-     }
-   
--  std::set<Junction, skip_count_lt> vseg_juncs[num_threads];
-+  std::set<Junction, skip_count_lt> vseg_juncs[1];
-   std::set<Junction, skip_count_lt> cov_juncs;
-   std::set<Junction, skip_count_lt> butterfly_juncs;
-   
-   std::set<Junction> juncs;
-   
--  std::set<Deletion> vdeletions[num_threads];
--  std::set<Insertion> vinsertions[num_threads];
--  FusionSimpleSet vfusions[num_threads];
-+  std::set<Deletion> vdeletions[1];
-+  std::set<Insertion> vinsertions[1];
-+  FusionSimpleSet vfusions[1];
-   
-   RefSequenceTable rt(sam_header, true);
-   
---- a/src/tophat_reports.cpp	2012-10-18 10:43:09.000000000 -0700
-+++ b/src/tophat_reports.cpp	2012-10-27 22:39:31.000000000 -0700
-@@ -2290,11 +2290,11 @@
- 	num_threads = 1;
-     }
- 
--  JunctionSet vjunctions[num_threads];
--  InsertionSet vinsertions[num_threads];
--  DeletionSet vdeletions[num_threads];
--  FusionSet vfusions[num_threads];
--  Coverage vcoverages[num_threads];
-+  JunctionSet vjunctions[1];
-+  InsertionSet vinsertions[1];
-+  DeletionSet vdeletions[1];
-+  FusionSet vfusions[1];
-+  Coverage vcoverages[1];
-   
-   vector<boost::thread*> threads;
-   for (int i = 0; i < num_threads; ++i)
-@@ -2420,10 +2420,10 @@
-     fprintf(stderr, "Warning: %lu small overhang junctions!\n", (long unsigned int)small_overhangs);
-   */
- 
--  JunctionSet vfinal_junctions[num_threads];
--  InsertionSet vfinal_insertions[num_threads];
--  DeletionSet vfinal_deletions[num_threads];
--  FusionSet vfinal_fusions[num_threads];
-+  JunctionSet vfinal_junctions[1];
-+  InsertionSet vfinal_insertions[1];
-+  DeletionSet vfinal_deletions[1];
-+  FusionSet vfinal_fusions[1];
- 
-   for (int i = 0; i < num_threads; ++i)
-     {
diff --git a/Library/Formula/velvet.rb b/Library/Formula/velvet.rb
deleted file mode 100644
index 6c42fe2db..000000000
--- a/Library/Formula/velvet.rb
+++ /dev/null
@@ -1,18 +0,0 @@
-require 'formula'
-
-class Velvet < Formula
-  homepage 'http://www.ebi.ac.uk/~zerbino/velvet/'
-  url 'http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.08.tgz'
-  sha1 'cef486759fa577d86ff67d70898ff330f5d0403c'
-
-  head 'https://github.com/dzerbino/velvet.git'
-
-  def install
-    inreplace 'Makefile' do |s|
-      # recommended in Makefile for compiling on Mac OS X
-      s.change_make_var! "CFLAGS", "-Wall -m64"
-    end
-    system "make velveth velvetg OPENMP=1 MAXKMERLENGTH=31 LONGSEQUENCES=1"
-    bin.install 'velveth', 'velvetg'
-  end
-end