bio-samtools 0.5.2 → 0.5.3

data/.travis.yml

@@ -0,0 +1,11 @@
+language: ruby
+before_install:
+  - sudo apt-get update
+  - sudo apt-get install zlib1g-dev libncurses5-dev libtinfo-dev
+before_script:
+  - cd ext
+  - ruby mkrf_conf.rb
+  - rake -f Rakefile
+  - cd ../
+rvm:
+  - 1.9.3

data/VERSION

@@ -1 +1 @@
-0.5.2
+0.5.3

data/bio-samtools.gemspec

@@ -4,21 +4,25 @@
 # -*- encoding: utf-8 -*-
 
 Gem::Specification.new do |s|
-  s.name = "bio-samtools"
-  s.version = "0.5.2"
+  s.name = %q{bio-samtools}
+  s.version = "0.5.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Ricardo Ramirez-Gonzalez", "Dan MacLean", "Raoul J.P. Bonnal"]
-  s.date = "2012-03-14"
-  s.description = "Binder of samtools for ruby, on the top of FFI. \n\n  This project was born from the need to add support of BAM files to \n  the gee_fu genome browser (http://github.com/danmaclean/gee_fu)."
-  s.email = "ilpuccio.febo@gmail.com"
-  s.extensions = ["ext/mkrf_conf.rb"]
+  s.authors = [%q{Ricardo Ramirez-Gonzalez}, %q{Dan MacLean}, %q{Raoul J.P. Bonnal}]
+  s.date = %q{2012-04-14}
+  s.description = %q{Binder of samtools for ruby, on the top of FFI. 
+
+  This project was born from the need to add support of BAM files to 
+  the gee_fu genome browser (http://github.com/danmaclean/gee_fu).}
+  s.email = %q{ilpuccio.febo@gmail.com}
+  s.extensions = [%q{ext/mkrf_conf.rb}]
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
   ]
   s.files = [
     ".document",
+    ".travis.yml",
     "Gemfile",
     "Gemfile.lock",
     "LICENSE.txt",
@@ -153,7 +157,6 @@ Gem::Specification.new do |s|
     "doc/tutorial.html",
     "doc/tutorial.pdf",
     "ext/Makefile-bioruby.patch",
-    "ext/Rakefile",
     "ext/mkrf_conf.rb",
     "lib/bio-samtools.rb",
     "lib/bio/.DS_Store",
@@ -191,11 +194,11 @@ Gem::Specification.new do |s|
     "test/test_bio-samtools.rb",
     "test/test_vcf.rb"
   ]
-  s.homepage = "http://github.com/helios/bioruby-samtools"
-  s.licenses = ["MIT"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.10"
-  s.summary = "Binder of samtools for ruby, on the top of FFI."
+  s.homepage = %q{http://github.com/helios/bioruby-samtools}
+  s.licenses = [%q{MIT}]
+  s.require_paths = [%q{lib}]
+  s.rubygems_version = %q{1.8.6}
+  s.summary = %q{Binder of samtools for ruby, on the top of FFI.}
 
   if s.respond_to? :specification_version then
     s.specification_version = 3

data/ext/Makefile-bioruby.patch

@@ -3,7 +3,7 @@
 @@ -1,10 +1,11 @@
  CC=			gcc
 -CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
-+CFLAGS=		-g -Wall -O2 -m64 -fPIC #-arch ppc
++CFLAGS=		-g -Wall -O2 -fPIC #-m64 #-fPIC #-arch ppc
  DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
  KNETFILE_O=	knetfile.o
  LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-samtools
 version: !ruby/object:Gem::Version
-  version: 0.5.2
+  version: 0.5.3
   prerelease: 
 platform: ruby
 authors:
@@ -11,11 +11,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-03-14 00:00:00.000000000 Z
+date: 2012-04-14 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
-  requirement: &2168700900 !ruby/object:Gem::Requirement
+  requirement: &2155890140 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -23,10 +23,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2168700900
+  version_requirements: *2155890140
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2168700160 !ruby/object:Gem::Requirement
+  requirement: &2153046360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -34,10 +34,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2168700160
+  version_requirements: *2153046360
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2168699180 !ruby/object:Gem::Requirement
+  requirement: &2153045200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -45,10 +45,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2168699180
+  version_requirements: *2153045200
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2168698320 !ruby/object:Gem::Requirement
+  requirement: &2153043840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -56,10 +56,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2168698320
+  version_requirements: *2153043840
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2168697320 !ruby/object:Gem::Requirement
+  requirement: &2153042320 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -67,10 +67,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2168697320
+  version_requirements: *2153042320
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2168696260 !ruby/object:Gem::Requirement
+  requirement: &2153039920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -78,10 +78,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2168696260
+  version_requirements: *2153039920
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2168695500 !ruby/object:Gem::Requirement
+  requirement: &2153031660 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -89,10 +89,10 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *2168695500
+  version_requirements: *2153031660
 - !ruby/object:Gem::Dependency
   name: ffi
-  requirement: &2152334180 !ruby/object:Gem::Requirement
+  requirement: &2153030200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -100,10 +100,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2152334180
+  version_requirements: *2153030200
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &2152333420 !ruby/object:Gem::Requirement
+  requirement: &2153028420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -111,7 +111,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2152333420
+  version_requirements: *2153028420
 description: ! "Binder of samtools for ruby, on the top of FFI. \n\n  This project
   was born from the need to add support of BAM files to \n  the gee_fu genome browser
   (http://github.com/danmaclean/gee_fu)."
@@ -124,6 +124,7 @@ extra_rdoc_files:
 - README.rdoc
 files:
 - .document
+- .travis.yml
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
@@ -258,7 +259,6 @@ files:
 - doc/tutorial.html
 - doc/tutorial.pdf
 - ext/Makefile-bioruby.patch
-- ext/Rakefile
 - ext/mkrf_conf.rb
 - lib/bio-samtools.rb
 - lib/bio/.DS_Store
@@ -310,7 +310,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -37499078565960311
+      hash: -2712419178803943908
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -319,7 +319,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 1.8.6
 signing_key: 
 specification_version: 3
 summary: Binder of samtools for ruby, on the top of FFI.

data/ext/Rakefile

@@ -1,55 +0,0 @@
-require 'rbconfig'
-require 'open-uri'
-require 'fileutils'
-include FileUtils::Verbose
-require 'rake/clean'
-
-URL = "http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2/download"
-
-task :download do
-  open(URL) do |uri|
-    File.open("samtools-0.1.18.tar.bz2",'wb') do |fout|
-      fout.write(uri.read)
-    end #fout 
-  end #uri
-end
-    
-task :compile do
-  sh "tar xvfj samtools-0.1.18.tar.bz2"
-  cd("samtools-0.1.18") do
-    sh "patch < ../Makefile-bioruby.patch"
-    case Config::CONFIG['host_os']
-      when /linux/
-        #sh "CFLAGS='-g -Wall -O2 -fPIC' make -e"
-        sh "make"
-        cp("libbam.a","/Users/macleand/bioruby-samtools/ext/../lib/bio/db/sam/external")
-        #sh "CFLAGS='-g -Wall -O2 -fPIC' make -e libbam.so.1-local"
-        sh "make libbam.so.1-local"
-        cp("samtools", "/Users/macleand/bioruby-samtools/ext/../lib/bio/db/sam/external")
-        cp("libbam.so.1","/Users/macleand/bioruby-samtools/ext/../lib/bio/db/sam/external")
-      when /darwin/
-        sh "make"
-        cp("libbam.a","/Users/macleand/bioruby-samtools/ext/../lib/bio/db/sam/external")
-        sh "make libbam.1.dylib-local"
-        cp("libbam.1.dylib","/Users/macleand/bioruby-samtools/ext/../lib/bio/db/sam/external")
-        sh "make"
-        cp('samtools', "/Users/macleand/bioruby-samtools/ext/../lib/bio/db/sam/external")      
-      when /mswin|mingw/ then raise NotImplementedError, "BWA library is not available for Windows platform"  
-    end #case
-  end #cd
-  cd("samtools-0.1.18/bcftools") do
-    sh "make"
-    cp('bcftools', "/Users/macleand/bioruby-samtools/ext/../lib/bio/db/sam/external")
-  end
-end
-  
-task :clean do
-  cd("samtools-0.1.18") do
-    sh "make clean"
-  end
-  rm("samtools-0.1.18.tar.bz2")
-  rm_rf("samtools-0.1.18")
-end
-
-task :default => [:download, :compile, :clean]
-