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Remove formulae moved to Homebrew-science

Closes #16143.
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commit 0e79d4fae6aeb5599a38d730e15d64088150b81a 1 parent a570325
@jacknagel jacknagel authored
Showing with 0 additions and 957 deletions.
  1. +0 −1  Library/Aliases/fsa
  2. +0 −50 Library/Formula/abyss.rb
  3. +0 −12 Library/Formula/arow++.rb
  4. +0 −70 Library/Formula/bamtools.rb
  5. +0 −39 Library/Formula/blast.rb
  6. +0 −12 Library/Formula/bowtie.rb
  7. +0 −84 Library/Formula/bwa.rb
  8. +0 −14 Library/Formula/cd-hit.rb
  9. +0 −15 Library/Formula/clustal-omega.rb
  10. +0 −12 Library/Formula/clustal-w.rb
  11. +0 −32 Library/Formula/cufflinks.rb
  12. +0 −12 Library/Formula/dadadodo.rb
  13. +0 −28 Library/Formula/emboss.rb
  14. +0 −23 Library/Formula/fast-statistical-alignment.rb
  15. +0 −32 Library/Formula/fastx_toolkit.rb
  16. +0 −31 Library/Formula/gmap-gsnap.rb
  17. +0 −23 Library/Formula/hmmer.rb
  18. +0 −129 Library/Formula/mira.rb
  19. +0 −18 Library/Formula/mrfast.rb
  20. +0 −37 Library/Formula/muscle.rb
  21. +0 −18 Library/Formula/paml.rb
  22. +0 −35 Library/Formula/phyml.rb
  23. +0 −15 Library/Formula/plink.rb
  24. +0 −14 Library/Formula/primer3.rb
  25. +0 −12 Library/Formula/prodigal.rb
  26. +0 −13 Library/Formula/quicktree.rb
  27. +0 −24 Library/Formula/samtools.rb
  28. +0 −35 Library/Formula/sga.rb
  29. +0 −15 Library/Formula/tabix.rb
  30. +0 −84 Library/Formula/tophat.rb
  31. +0 −18 Library/Formula/velvet.rb
View
1  Library/Aliases/fsa
View
50 Library/Formula/abyss.rb
@@ -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]);
- }
View
12 Library/Formula/arow++.rb
@@ -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
View
70 Library/Formula/bamtools.rb
@@ -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
View
39 Library/Formula/blast.rb
@@ -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
View
12 Library/Formula/bowtie.rb
@@ -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
View
84 Library/Formula/bwa.rb
@@ -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);
View
14 Library/Formula/cd-hit.rb
@@ -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
View
15 Library/Formula/clustal-omega.rb
@@ -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
View
12 Library/Formula/clustal-w.rb
@@ -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
View
32 Library/Formula/cufflinks.rb
@@ -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
View
12 Library/Formula/dadadodo.rb
@@ -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
View
28 Library/Formula/emboss.rb
@@ -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
View
23 Library/Formula/fast-statistical-alignment.rb
@@ -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
View
32 Library/Formula/fastx_toolkit.rb
@@ -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
View
31 Library/Formula/gmap-gsnap.rb
@@ -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
View
23 Library/Formula/hmmer.rb
@@ -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
View
129 Library/Formula/mira.rb
@@ -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 );
- }
View
18 Library/Formula/mrfast.rb
@@ -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
View
37 Library/Formula/muscle.rb
@@ -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;
View
18 Library/Formula/paml.rb
@@ -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
View
35 Library/Formula/phyml.rb
@@ -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
View
15 Library/Formula/plink.rb
@@ -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
View
14 Library/Formula/primer3.rb
@@ -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
View
12 Library/Formula/prodigal.rb
@@ -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
View
13 Library/Formula/quicktree.rb
@@ -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
View
24 Library/Formula/samtools.rb
@@ -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
View
35 Library/Formula/sga.rb
@@ -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
View
15 Library/Formula/tabix.rb
@@ -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
View
84 Library/Formula/tophat.rb
@@ -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)
- {
View
18 Library/Formula/velvet.rb
@@ -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
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