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Remove science formula #13630

Closed
wants to merge 2 commits into from

3 participants

@audy

Removed science formula listed in issue #13472

@audy

Where is the change commits button?

@samueljohn

To change commit you have to read about git rebase -i and then git push --force.
I can't explain it here - there a tons of good online tutorials.

I think we should not just delete all of these as long as the ones we think might be still of use should go into homebrew/science. Is there a pull request over at homebrew/science?

@adamv
Owner

Can't pull this without seeing that they've all been migrated to Homebrew-science first.

@adamv adamv closed this
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Commits on Jul 26, 2012
  1. @audy

    - Resolve issue Homebrew/homebrew#13594 (md5 changed).

    audy authored
    - MAXKMERLENGTH should be 31 not 1.
  2. @audy

    removed science formula

    audy authored
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View
111 Library/Formula/blast.rb
@@ -1,111 +0,0 @@
-require 'formula'
-
-class Blast < Formula
- homepage 'http://blast.ncbi.nlm.nih.gov/'
- url 'ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.2.25/ncbi-blast-2.2.25+-src.tar.gz'
- version '2.2.25'
- md5 '01256b808e3af49a5087945b6a8c8293'
-
- fails_with :clang do
- build 318
- end
-
- def options
- [['--with-dll', "Create dynamic binaries instead of static"]]
- end
-
- # fixes to 2.2.25 acknowledged upstream by Aaron U. per email
- # inform configure about -Os
- def patches
- DATA
- end
-
- def install
- args = ["--prefix=#{prefix}"]
- args << "--with-dll" if ARGV.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
-
-__END__
----
- c++/src/build-system/configure | 24 ++++++++++++------------
- 1 file changed, 12 insertions(+), 12 deletions(-)
-
-diff --git a/c++/src/build-system/configure b/c++/src/build-system/configure
-index 2f467a2..a2d14c7 100755
---- a/c++/src/build-system/configure
-+++ b/c++/src/build-system/configure
-@@ -8538,29 +8538,29 @@ fi
- if test "$compiler" != "MSVC" ; then
- if test "$with_debug" = "no" ; then
- with_optimization=${with_optimization:="yes"}
-- CFLAGS=` echo " $CFLAGS" | sed 's/[ ]-g[0-9]*//g'`
-- CXXFLAGS=`echo " $CXXFLAGS" | sed 's/[ ]-g[0-9]*//g'`
-- LDFLAGS=` echo " $LDFLAGS" | sed 's/[ ]-g[0-9]*//g'`
-+ CFLAGS=` echo " $CFLAGS" | sed 's/[ ]-g[0-9s]*//g'`
-+ CXXFLAGS=`echo " $CXXFLAGS" | sed 's/[ ]-g[0-9s]*//g'`
-+ LDFLAGS=` echo " $LDFLAGS" | sed 's/[ ]-g[0-9s]*//g'`
- CPPFLAGS="-DNDEBUG $CPPFLAGS"
- else
- with_optimization=${with_optimization:="no"}
-- if echo " $CFLAGS" |grep -v >/dev/null '[ ]-g[0-9]*' ; then
-+ if echo " $CFLAGS" |grep -v >/dev/null '[ ]-g[0-9s]*' ; then
- CFLAGS="$CFLAGS -g" ; fi
-- if echo " $CXXFLAGS" |grep -v >/dev/null '[ ]-g[0-9]*' ; then
-+ if echo " $CXXFLAGS" |grep -v >/dev/null '[ ]-g[0-9s]*' ; then
- CXXFLAGS="$CXXFLAGS -g" ; fi
- if test "${with_tcheck=no}" = "no" ; then
- CPPFLAGS="-D_DEBUG $CPPFLAGS"
- else
- CPPFLAGS="-DNDEBUG $CPPFLAGS"
- fi
-- if echo " $LDFLAGS" |grep -v >/dev/null '[ ]-g[0-9]*' ;
-+ if echo " $LDFLAGS" |grep -v >/dev/null '[ ]-g[0-9s]*' ;
- then LDFLAGS="$LDFLAGS -g" ; fi
- STRIP="@:"
- fi
-
-- NOPT_CFLAGS=` echo " $CFLAGS" | sed 's/[ ]-x*O[0-9]*//g'`
-- NOPT_CXXFLAGS=`echo " $CXXFLAGS" | sed 's/[ ]-x*O[0-9]*//g'`
-- NOPT_LDFLAGS=` echo " $LDFLAGS" | sed 's/[ ]-x*O[0-9]*//g'`
-+ NOPT_CFLAGS=` echo " $CFLAGS" | sed 's/[ ]-x*O[0-9s]*//g'`
-+ NOPT_CXXFLAGS=`echo " $CXXFLAGS" | sed 's/[ ]-x*O[0-9s]*//g'`
-+ NOPT_LDFLAGS=` echo " $LDFLAGS" | sed 's/[ ]-x*O[0-9s]*//g'`
- if test "${with_tcheck-no}" != "no"; then
- # Suppress warnings when building with ICC.
- NOPT_CFLAGS="$NOPT_CFLAGS -O0"
-@@ -8575,11 +8575,11 @@ if test "$compiler" != "MSVC" ; then
- FAST_CXXFLAGS="$CXXFLAGS"
- FAST_LDFLAGS="$LDFLAGS"
- else
-- if echo " $CFLAGS" |grep -v >/dev/null '[ ]-x*O[0-9]*' ; then
-+ if echo " $CFLAGS" |grep -v >/dev/null '[ ]-x*O[0-9s]*' ; then
- CFLAGS="$CFLAGS -O" ; fi
-- if echo " $CXXFLAGS" |grep -v >/dev/null '[ ]-x*O[0-9]*' ; then
-+ if echo " $CXXFLAGS" |grep -v >/dev/null '[ ]-x*O[0-9s]*' ; then
- CXXFLAGS="$CXXFLAGS -O" ; fi
-- if echo " $LDFLAGS" |grep -v >/dev/null '[ ]-x*O[0-9]*' ; then
-+ if echo " $LDFLAGS" |grep -v >/dev/null '[ ]-x*O[0-9s]*' ; then
- LDFLAGS="$LDFLAGS -O" ; fi
- FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS"
- FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS"
---
-1.7.9.2
-
View
12 Library/Formula/bowtie.rb
@@ -1,12 +0,0 @@
-require 'formula'
-
-class Bowtie < Formula
- url 'http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip'
- homepage 'http://bowtie-bio.sourceforge.net/index.shtml'
- md5 '2808d61eaf15c9f7138794766c99a561'
-
- def install
- system "make"
- bin.install %W(bowtie bowtie-build bowtie-inspect)
- end
-end
View
15 Library/Formula/bwa.rb
@@ -1,15 +0,0 @@
-require 'formula'
-
-class Bwa < Formula
- homepage 'http://bio-bwa.sourceforge.net/'
- url 'http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.10.tar.bz2'
- md5 '04962f916f761dc259d9fb2452b46c5d'
-
- head 'https://github.com/lh3/bwa.git'
-
- def install
- system "make", "CC=#{ENV.cc}", "CFLAGS=#{ENV.cflags}"
- bin.install "bwa"
- man1.install "bwa.1"
- end
-end
View
12 Library/Formula/clustal-w.rb
@@ -1,12 +0,0 @@
-require 'formula'
-
-class ClustalW < Formula
- url 'http://www.clustal.org/download/2.0.12/clustalw-2.0.12.tar.gz'
- homepage 'http://www.clustal.org/'
- md5 '8d0c50ffbe5898b03509aa0a7709f642'
-
- def install
- system "./configure", "--disable-dependency-tracking", "--prefix=#{prefix}"
- system "make install"
- end
-end
View
12 Library/Formula/emboss.rb
@@ -1,12 +0,0 @@
-require 'formula'
-
-class Emboss < Formula
- url 'ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.4.0.tar.gz'
- homepage 'http://emboss.sourceforge.net/'
- md5 '54993a22064222b01bd4fc8086f7684d'
-
- def install
- system "./configure", "--prefix=#{prefix}", "--disable-debug", "--disable-dependency-tracking"
- system "make install"
- end
-end
View
12 Library/Formula/fast-statistical-alignment.rb
@@ -1,12 +0,0 @@
-require 'formula'
-
-class FastStatisticalAlignment < Formula
- url 'http://downloads.sourceforge.net/project/fsa/fsa-1.15.3.tar.gz'
- homepage 'http://fsa.sourceforge.net/'
- md5 '9c03a6b48c3a276f6233dc5715ed3d0a'
-
- 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.tar.bz2'
- md5 '6d233ff4ae3d52c457d447179f073a56'
-
- 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
15 Library/Formula/muscle.rb
@@ -1,15 +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'
- md5 'f767f00fd15f0c5db944d41936779e10'
-
- def install
- cd "src" do
- system "make"
- bin.install "muscle"
- end
- end
-end
View
14 Library/Formula/primer3.rb
@@ -1,14 +0,0 @@
-require 'formula'
-
-class Primer3 < Formula
- homepage 'http://primer3.sourceforge.net/'
- url 'http://downloads.sourceforge.net/project/primer3/primer3/2.2.3/primer3-2.2.3.tar.gz'
- md5 'b9cdcff68637479c094844d652c03839'
-
- 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
- url 'http://prodigal.googlecode.com/files/prodigal.v2_00.tar.gz'
- homepage 'http://prodigal.ornl.gov/'
- md5 'd110bd6a28004fc6ba4d13066b6103e2'
-
- def install
- system "make"
- bin.install 'prodigal'
- end
-end
View
18 Library/Formula/velvet.rb
@@ -1,18 +0,0 @@
-require 'formula'
-
-class Velvet < Formula
- url 'http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.03.tgz'
- homepage 'http://www.ebi.ac.uk/~zerbino/velvet/'
- md5 'ed1eaea940eff649bc8031f2cc7b78b5'
-
- 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=1 LONGSEQUENCES=1"
- bin.install 'velveth', 'velvetg'
- end
-end
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