diff options
Diffstat (limited to 'Library')
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 |