bio-samtools 0.2.0 → 0.2.1

data/Gemfile

@@ -3,6 +3,7 @@ source "http://rubygems.org"
 # Example:
 #   gem "activesupport", ">= 2.3.5"
 gem "ffi"
+gem "bio", ">= 1.4.1"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/README.rdoc

@@ -58,11 +58,8 @@ Ricardo dot Ramirez-Gonzalez at bbsrc dot ac dot uk
 -Operating system independent, DONE ( test needed)
 
 == IMPORTANT NOTE
--Libraries are compiled for 64 bit machines
--The gem/archive comes with preinstalled library .a and dylib, .dll is missing I didn't compile it.
+-Libraries are downloaded, compiled and installed inside the gem at install time on the host system
 -Library .a, I didn't check if it works on linux (test needed) 
--Library libbam.so.1, The library is simply compiled with make dylib without any special parameter on
-CentOS5.5 x86_64, gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48). 
 $ openssl dgst libbam.so.1
 MD5(libbam.so.1)= c45cfccfb41ffeb2730ee4b227d244c4
 
@@ -78,6 +75,17 @@ MD5(libbam.so.1)= c45cfccfb41ffeb2730ee4b227d244c4
 * Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
 * Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
 
+=== Important Notes for developers
+
+Remember that you must compile and install the right libbam library for you host system. In order to do that there are three possible solutions:
+* download, compile and install the library in bioruby-samtools-your_clone/lib/bio/db/sam/external/libbam.xxxxx by yourself
+* install the gem and then grab the compiled library cp `locate libbam.1.dylib` bioruby-samtools-your_clone/lib/bio/db/sam/external (library name is an example)
+* in your bioruby-samtools-your_clone create the Rakefile typing "cd ext; ruby mkrf_conf.rb; rake -f Rakefile"
+
+The latest I think is the easiest way, cause you are replicating the automatic process.
+
+For testing just run `rake test`. Tests must be improved.
+
 == Copyright
 
 Copyright (c) 2011 Raoul J.P. Bonnal. See LICENSE.txt for

data/VERSION

@@ -1 +1 @@
-0.2.0
+0.2.1

data/bio-samtools.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-samtools}
-  s.version = "0.2.0"
+  s.version = "0.2.1"
 
   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 = %q{2011-05-23}
+  s.date = %q{2011-05-27}
   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 
@@ -77,6 +77,7 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<ffi>, [">= 0"])
+      s.add_runtime_dependency(%q<bio>, [">= 1.4.1"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
       s.add_development_dependency(%q<jeweler>, [">= 0"])
@@ -85,6 +86,7 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<ffi>, [">= 0"])
     else
       s.add_dependency(%q<ffi>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.1"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<bundler>, ["~> 1.0.0"])
       s.add_dependency(%q<jeweler>, [">= 0"])
@@ -94,6 +96,7 @@ Gem::Specification.new do |s|
     end
   else
     s.add_dependency(%q<ffi>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.1"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<bundler>, ["~> 1.0.0"])
     s.add_dependency(%q<jeweler>, [">= 0"])

metadata

@@ -2,7 +2,7 @@
 name: bio-samtools
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.2.0
+  version: 0.2.1
 platform: ruby
 authors: 
 - Ricardo Ramirez-Gonzalez
@@ -12,7 +12,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-05-23 00:00:00 +02:00
+date: 2011-05-27 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -27,8 +27,19 @@ dependencies:
   prerelease: false
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
-  name: shoulda
+  name: bio
   requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.4.1
+  type: :runtime
+  prerelease: false
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: shoulda
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -36,10 +47,10 @@ dependencies:
         version: "0"
   type: :development
   prerelease: false
-  version_requirements: *id002
+  version_requirements: *id003
 - !ruby/object:Gem::Dependency 
   name: bundler
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -47,10 +58,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *id003
+  version_requirements: *id004
 - !ruby/object:Gem::Dependency 
   name: jeweler
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -58,10 +69,10 @@ dependencies:
         version: "0"
   type: :development
   prerelease: false
-  version_requirements: *id004
+  version_requirements: *id005
 - !ruby/object:Gem::Dependency 
   name: rcov
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  requirement: &id006 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -69,10 +80,10 @@ dependencies:
         version: "0"
   type: :development
   prerelease: false
-  version_requirements: *id005
+  version_requirements: *id006
 - !ruby/object:Gem::Dependency 
   name: bio
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  requirement: &id007 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -80,10 +91,10 @@ dependencies:
         version: 1.4.1
   type: :development
   prerelease: false
-  version_requirements: *id006
+  version_requirements: *id007
 - !ruby/object:Gem::Dependency 
   name: ffi
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  requirement: &id008 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -91,7 +102,7 @@ dependencies:
         version: "0"
   type: :development
   prerelease: false
-  version_requirements: *id007
+  version_requirements: *id008
 description: |-
   Binder of samtools for ruby, on the top of FFI. 
   
@@ -164,7 +175,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: -2254602407450598476
+      hash: -1847812567454850000
       segments: 
       - 0
       version: "0"