bio-ngs 0.4.7.alpha.03 → 0.5.0

data/Rakefile

@@ -53,8 +53,4 @@ Rake::RDocTask.new do |rdoc|
 end
 
 require 'rspec/core/rake_task'
-RSpec::Core::RakeTask.new
-
-
-require 'development_tasks'
-BioNgs::BioNgsTasks.new
+RSpec::Core::RakeTask.new

data/VERSION

@@ -1 +1 @@
-0.4.7.alpha.03
+0.5.0

data/bio-ngs.gemspec

@@ -5,25 +5,25 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-ngs"
-  s.version = "0.4.7.alpha.03"
+  s.version = "0.5.0"
 
-  s.required_rubygems_version = Gem::Requirement.new("> 1.3.1") if s.respond_to? :required_rubygems_version=
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Francesco Strozzi", "Raoul J.P. Bonnal"]
-  s.date = "2012-05-29"
+  s.date = "2012-06-04"
   s.description = "bio-ngs provides a framework for handling NGS data with BioRuby"
   s.email = "francesco.strozzi@gmail.com"
   s.executables = ["biongs"]
   s.extensions = ["ext/mkrf_conf.rb"]
   s.extra_rdoc_files = [
     "LICENSE.txt",
-    "README.rdoc"
+    "README.md"
   ]
   s.files = [
     ".document",
     "Gemfile",
     "Gemfile.lock",
     "LICENSE.txt",
-    "README.rdoc",
+    "README.md",
     "Rakefile",
     "VERSION",
     "bin/biongs",
@@ -34,6 +34,7 @@ Gem::Specification.new do |s|
     "features/illumina_project_rebuild.feature",
     "features/step_definitions/cufflinks_gtf.rb",
     "features/step_definitions/cufflinks_gtf_parser_indexing.rb",
+    "features/step_definitions/illumina_project_rebuild.rb",
     "features/support/env.rb",
     "lib/bio-ngs.rb",
     "lib/bio/appl/ngs/bcftools.rb",
@@ -78,7 +79,6 @@ Gem::Specification.new do |s|
     "lib/bio/ngs/record.rb",
     "lib/bio/ngs/task.rb",
     "lib/bio/ngs/utils.rb",
-    "lib/development_tasks.rb",
     "lib/enumerable.rb",
     "lib/meta.rb",
     "lib/tasks/bwa.thor",
@@ -86,6 +86,7 @@ Gem::Specification.new do |s|
     "lib/tasks/filter.thor",
     "lib/tasks/history.thor",
     "lib/tasks/homology.thor",
+    "lib/tasks/install.thor",
     "lib/tasks/ontology.thor",
     "lib/tasks/pre.thor",
     "lib/tasks/project.thor",
@@ -201,17 +202,19 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<daemons>, [">= 1.1.0"])
       s.add_runtime_dependency(%q<ruby-ensembl-api>, [">= 1.0.1"])
       s.add_runtime_dependency(%q<activerecord>, [">= 3.0.5"])
-      s.add_runtime_dependency(%q<sqlite3>, [">= 1.3.3"])
-      s.add_runtime_dependency(%q<bio-blastxmlparser>, [">= 0"])
       s.add_runtime_dependency(%q<progressbar>, [">= 0.9.0"])
       s.add_runtime_dependency(%q<rake>, ["= 0.9.2.2"])
       s.add_runtime_dependency(%q<json>, [">= 0"])
       s.add_runtime_dependency(%q<parallel>, [">= 0"])
+      s.add_runtime_dependency(%q<bio-blastxmlparser>, [">= 0"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<bundler>, ["~> 1.1.0"])
       s.add_development_dependency(%q<jeweler>, ["~> 1.8.3"])
       s.add_development_dependency(%q<rcov>, ["~> 0.9.11"])
       s.add_development_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_development_dependency(%q<jdbc-sqlite3>, [">= 0"])
+      s.add_development_dependency(%q<activerecord-jdbcsqlite3-adapter>, [">= 0"])
+      s.add_development_dependency(%q<sqlite3>, [">= 0"])
       s.add_development_dependency(%q<thor>, ["= 0.14.6"])
       s.add_development_dependency(%q<ffi>, [">= 1.0.6"])
       s.add_development_dependency(%q<rubyvis>, [">= 0.5.0"])
@@ -220,12 +223,11 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<bio-samtools>, [">= 0.3.2"])
       s.add_development_dependency(%q<ruby-ensembl-api>, [">= 1.0.1"])
       s.add_development_dependency(%q<activerecord>, [">= 3.0.5"])
-      s.add_development_dependency(%q<sqlite3>, [">= 1.3.3"])
-      s.add_development_dependency(%q<bio-blastxmlparser>, [">= 0"])
       s.add_development_dependency(%q<progressbar>, [">= 0.9.0"])
       s.add_development_dependency(%q<json>, [">= 0"])
       s.add_development_dependency(%q<rake>, ["= 0.9.2.2"])
       s.add_development_dependency(%q<parallel>, [">= 0"])
+      s.add_development_dependency(%q<bio-blastxmlparser>, [">= 0"])
     else
       s.add_dependency(%q<bio>, [">= 1.4.2"])
       s.add_dependency(%q<bio-samtools>, [">= 0.3.2"])
@@ -234,17 +236,19 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<daemons>, [">= 1.1.0"])
       s.add_dependency(%q<ruby-ensembl-api>, [">= 1.0.1"])
       s.add_dependency(%q<activerecord>, [">= 3.0.5"])
-      s.add_dependency(%q<sqlite3>, [">= 1.3.3"])
-      s.add_dependency(%q<bio-blastxmlparser>, [">= 0"])
       s.add_dependency(%q<progressbar>, [">= 0.9.0"])
       s.add_dependency(%q<rake>, ["= 0.9.2.2"])
       s.add_dependency(%q<json>, [">= 0"])
       s.add_dependency(%q<parallel>, [">= 0"])
+      s.add_dependency(%q<bio-blastxmlparser>, [">= 0"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<bundler>, ["~> 1.1.0"])
       s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
       s.add_dependency(%q<rcov>, ["~> 0.9.11"])
       s.add_dependency(%q<bio>, [">= 1.4.2"])
+      s.add_dependency(%q<jdbc-sqlite3>, [">= 0"])
+      s.add_dependency(%q<activerecord-jdbcsqlite3-adapter>, [">= 0"])
+      s.add_dependency(%q<sqlite3>, [">= 0"])
       s.add_dependency(%q<thor>, ["= 0.14.6"])
       s.add_dependency(%q<ffi>, [">= 1.0.6"])
       s.add_dependency(%q<rubyvis>, [">= 0.5.0"])
@@ -253,12 +257,11 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<bio-samtools>, [">= 0.3.2"])
       s.add_dependency(%q<ruby-ensembl-api>, [">= 1.0.1"])
       s.add_dependency(%q<activerecord>, [">= 3.0.5"])
-      s.add_dependency(%q<sqlite3>, [">= 1.3.3"])
-      s.add_dependency(%q<bio-blastxmlparser>, [">= 0"])
       s.add_dependency(%q<progressbar>, [">= 0.9.0"])
       s.add_dependency(%q<json>, [">= 0"])
       s.add_dependency(%q<rake>, ["= 0.9.2.2"])
       s.add_dependency(%q<parallel>, [">= 0"])
+      s.add_dependency(%q<bio-blastxmlparser>, [">= 0"])
     end
   else
     s.add_dependency(%q<bio>, [">= 1.4.2"])
@@ -268,17 +271,19 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<daemons>, [">= 1.1.0"])
     s.add_dependency(%q<ruby-ensembl-api>, [">= 1.0.1"])
     s.add_dependency(%q<activerecord>, [">= 3.0.5"])
-    s.add_dependency(%q<sqlite3>, [">= 1.3.3"])
-    s.add_dependency(%q<bio-blastxmlparser>, [">= 0"])
     s.add_dependency(%q<progressbar>, [">= 0.9.0"])
     s.add_dependency(%q<rake>, ["= 0.9.2.2"])
     s.add_dependency(%q<json>, [">= 0"])
     s.add_dependency(%q<parallel>, [">= 0"])
+    s.add_dependency(%q<bio-blastxmlparser>, [">= 0"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<bundler>, ["~> 1.1.0"])
     s.add_dependency(%q<jeweler>, ["~> 1.8.3"])
     s.add_dependency(%q<rcov>, ["~> 0.9.11"])
     s.add_dependency(%q<bio>, [">= 1.4.2"])
+    s.add_dependency(%q<jdbc-sqlite3>, [">= 0"])
+    s.add_dependency(%q<activerecord-jdbcsqlite3-adapter>, [">= 0"])
+    s.add_dependency(%q<sqlite3>, [">= 0"])
     s.add_dependency(%q<thor>, ["= 0.14.6"])
     s.add_dependency(%q<ffi>, [">= 1.0.6"])
     s.add_dependency(%q<rubyvis>, [">= 0.5.0"])
@@ -287,12 +292,11 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<bio-samtools>, [">= 0.3.2"])
     s.add_dependency(%q<ruby-ensembl-api>, [">= 1.0.1"])
     s.add_dependency(%q<activerecord>, [">= 3.0.5"])
-    s.add_dependency(%q<sqlite3>, [">= 1.3.3"])
-    s.add_dependency(%q<bio-blastxmlparser>, [">= 0"])
     s.add_dependency(%q<progressbar>, [">= 0.9.0"])
     s.add_dependency(%q<json>, [">= 0"])
     s.add_dependency(%q<rake>, ["= 0.9.2.2"])
     s.add_dependency(%q<parallel>, [">= 0"])
+    s.add_dependency(%q<bio-blastxmlparser>, [">= 0"])
   end
 end
 

data/features/illumina_project_rebuild.feature

@@ -5,8 +5,7 @@ As a bioinformatician
 I want to have a querable data structure which represents most of the pre cumputed data
 
 Scenario: Explore and Build data structure
-  Given A path with many projects at the first level
-  And others at second level (inside others directories)
+  Given A path with many projects at the first and second level
   When I build the projects structure
   Then I sould get all the projects organized in the same structure.
 

data/features/step_definitions/cufflinks_gtf.rb

@@ -27,4 +27,9 @@ end
 
 Then /^I want to "(.*?)" the "(.*?)" in each subdirectory$/ do |arg1, arg2|
   pending # express the regexp above with the code you wish you had
+end
+
+
+Then /^I want to save "(.*?)" in single files formatted in "(.*?)" format$/ do |arg1, arg2|
+  pending # express the regexp above with the code you wish you had
 end

data/features/step_definitions/illumina_project_rebuild.rb

@@ -0,0 +1,20 @@
+
+
+Given /^A path with many projects at the first and second level$/ do
+  @projects_path =  File.join(File.dirname(__FILE__),'../../test/data')
+  @projects_path.should match '.*/bioruby-ngs/features/step_definitions/../../test/data'
+end
+
+When /^I build the projects structure$/ do
+   @projects = Bio::Ngs::Illumina.build @projects_path
+
+   @projects.should_not be nil
+end
+
+Then /^I sould get all the projects organized in the same structure\.$/ do
+	@data_json = @projects.to_json
+	@fixed_json = @data_json.gsub(/\"name\":\".*?\",/,"\"name\":\"test\",").gsub(/\"........-....-....-....-............\":/,"\"retest\":")
+    @fixed_json.should == <<JSON
+"{\"json_class\":\"Bio::Ngs::Illumina::Projects\",\"name\":\"test\",\"pool\":{\"Cow\":{\"json_class\":\"Bio::Ngs::Illumina::Project\",\"name\":\"test\",\"sample_sheet\":null,\"samples\":{\"SQ_0007\":{\"json_class\":\"Bio::Ngs::Illumina::Sample\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"path\":\"Sample_SQ_0007\"},\"files\":{\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"filtered/SQ_0007_CGATGT_L003_R1_001.fastq.gz\",\"filtered\":true,\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"filtered/SQ_0007_CGATGT_L003_R1_002.fastq.gz\",\"filtered\":true,\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"filtered/SQ_0007_CGATGT_L003_R2_001.fastq.gz\",\"filtered\":true,\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"filtered/SQ_0007_CGATGT_L003_R2_002.fastq.gz\",\"filtered\":true,\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0007_CGATGT_L003_R1_001.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0007_CGATGT_L003_R1_002.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0007_CGATGT_L003_R2_001.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0007_CGATGT_L003_R2_002.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"trimmed/SQ_0007_CGATGT_L003_R1_TRIMMED.fastq.gz\",\"trimmed\":true,\"trimmed_aggregated\":true,\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"trimmed/SQ_0007_CGATGT_L003_R2_TRIMMED.fastq.gz\",\"trimmed\":true,\"trimmed_aggregated\":true,\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\"}}}},\"SQ_0008\":{\"json_class\":\"Bio::Ngs::Illumina::Sample\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"path\":\"Sample_SQ_0008\"},\"files\":{\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0008_CGATGT_L003_R1_001.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0008_CGATGT_L003_R1_002.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0008_CGATGT_L003_R2_001.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0008_CGATGT_L003_R2_002.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}}}},\"SQ_0009\":{\"json_class\":\"Bio::Ngs::Illumina::Sample\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"path\":\"Sample_SQ_0009\"},\"files\":{\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0009_CGATGT_L003_R1_001.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0009_CGATGT_L003_R1_002.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0009_CGATGT_L003_R2_001.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0009_CGATGT_L003_R2_002.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}}}}}},\"Dog\":{\"json_class\":\"Bio::Ngs::Illumina::Project\",\"name\":\"test\",\"sample_sheet\":null,\"samples\":{\"SQ_0004\":{\"json_class\":\"Bio::Ngs::Illumina::Sample\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"path\":\"Sample_SQ_0004\"},\"files\":{\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0004_CGATGT_L003_R1_001.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0004_CGATGT_L003_R1_002.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0004_CGATGT_L003_R2_001.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0004_CGATGT_L003_R2_002.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}}}},\"SQ_0005\":{\"json_class\":\"Bio::Ngs::Illumina::Sample\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"path\":\"Sample_SQ_0005\"},\"files\":{\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0005_CGATGT_L003_R1_001.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0005_CGATGT_L003_R1_002.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0005_CGATGT_L003_R2_001.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0005_CGATGT_L003_R2_002.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}}}},\"SQ_0006\":{\"json_class\":\"Bio::Ngs::Illumina::Sample\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"path\":\"Sample_SQ_0006\"},\"files\":{\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0006_CGATGT_L003_R1_001.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0006_CGATGT_L003_R1_002.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0006_CGATGT_L003_R2_001.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0006_CGATGT_L003_R2_002.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}}}}}},\"Human\":{\"json_class\":\"Bio::Ngs::Illumina::Project\",\"name\":\"test\",\"sample_sheet\":null,\"samples\":{\"SQ_0001\":{\"json_class\":\"Bio::Ngs::Illumina::Sample\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"path\":\"Sample_SQ_0001\"},\"files\":{\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0001_CGATGT_L003_R1_001.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0001_CGATGT_L003_R1_002.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0001_CGATGT_L003_R2_001.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0001_CGATGT_L003_R2_002.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}}}},\"SQ_0002\":{\"json_class\":\"Bio::Ngs::Illumina::Sample\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"path\":\"Sample_SQ_0002\"},\"files\":{\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0002_CGATGT_L003_R1_001.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0002_CGATGT_L003_R1_002.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0002_CGATGT_L003_R2_001.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0002_CGATGT_L003_R2_002.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}}}},\"SQ_0003\":{\"json_class\":\"Bio::Ngs::Illumina::Sample\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"path\":\"Sample_SQ_0003\"},\"files\":{\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0003_CGATGT_L003_R1_001.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0003_CGATGT_L003_R1_002.fastq.gz\",\"left\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0003_CGATGT_L003_R2_001.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"001\"}},\"retest\":{\"json_class\":\"Bio::Ngs::Illumina::MetaReads\",\"name\":\"test\",\"metadata\":{\"name\":\"test\",\"filename\":\"SQ_0003_CGATGT_L003_R2_002.fastq.gz\",\"right\":true,\"zipped\":true,\"index\":\"CGATGT\",\"lane\":\"003\",\"chunks\":\"002\"}}}}}}}}"
+JSON
+end

data/lib/bio-ngs.rb

@@ -22,8 +22,12 @@ require 'thor/runner'
 require 'bio-blastxmlparser'
 require 'bio'
 require 'active_record'
-require 'sqlite3'
 
+if defined?(JRUBY_VERSION)
+	require 'jdbc-sqlite3'
+else
+	require 'sqlite3'
+end
 #Generic classes
 require 'enumerable'
 require 'wrapper'

data/lib/bio/appl/ngs/cufflinks/gtf/gtf_parser.rb

@@ -162,10 +162,6 @@ module Bio
             # t_idx=(f_lno-t.exons.size-2)
             idx[:transcripts] << t.byte_length
             idx[:names][t.attributes[:transcript_id]] = idx[:transcripts].length
-            if t.attributes[:transcript_id]=="ENST00000408219"
-              puts t.attributes[:transcript_id]
-              puts idx[:transcripts].length
-            end
             # eidx_b = t_idx +1
             # t.exons.each_index do |ei|
             #   idx[t_idx] << eidx_b + ei

data/lib/bio/ngs/homology.rb

@@ -99,4 +99,4 @@ module Bio
       
     end
   end
-end
+end

data/lib/bio/ngs/illumina/illumina.rb

@@ -41,7 +41,7 @@ module Bio
 
           Dir.chdir(path) do
             Dir.glob(["**/Project_*","**/Undetermined_indices"]).each do |project_dir|
-              project = Project.new(project_dir.basename.sub(/Project_/,""),project_dir)
+              project = Project.new(project_dir.sub(/.*Project_/,""),project_dir)
               projects.add(project)
               Dir.chdir(project_dir) do
                 Dir.glob("Sample*").each do |sample_dir|

data/lib/bio/ngs/illumina/sample.rb

@@ -18,12 +18,11 @@ module Bio
             "json_class"   => self.class.name,
             "name"         => name,
             "metadata"     => metadata
-            #{}"filenames"    => filenames_paths
           }.to_json(*a)
         end
 
         def self.json_create(o)
-          me = new(o["name"], o["metadata"]["path"],o["metadata"]["parent"])
+          me = new(o["name"], o["metadata"])
         end
       end #File
 

data/lib/meta.rb

@@ -48,6 +48,10 @@ module Meta
         "metadata"    => metadata
       }.to_json(*a)
     end
+
+    def self.json_create(o)
+      me = new(o["name"], o["metadata"])
+    end
     # end #Data
 
     # class File
@@ -75,12 +79,13 @@ module Meta
         "json_class"   => self.class.name,
         "name"         => name,
         "pool"     => pool
-        #{}"filenames"    => filenames_paths
       }.to_json(*a)
     end
 
     def self.json_create(o)
-      me = new(o["name"], o["metadata"]["path"],o["metadata"]["parent"])
+      me = new(o["name"])
+      me.pool=o["pool"]
+      me
     end
 
     def each &block

data/lib/tasks/install.thor

@@ -0,0 +1,14 @@
+class Install < Thor
+	
+		
+		desc "tools","Download and install NGS tools"
+		def tools
+			gem_path = File.expand_path(File.join(File.dirname(__FILE__),"..","..","ext"))
+			Dir.chdir gem_path
+    	load 'mkrf_conf.rb'
+    	`rake -f Rakefile`
+    	FileUtils.remove("Rakefile")
+		end
+	
+end
+

data/lib/tasks/project.thor

@@ -15,9 +15,9 @@ class Project < Thor
   end
     
   attr_accessor :name
-  
+  attr_accessor :adapter 
   desc "new [NAME]","Create a new NGS project directory"
-  method_option :type, :type => :string, :desc => "The project type (e.g. annotation)"
+  #method_option :type, :type => :string, :desc => "The project type (e.g. annotation)"
   def new(name)
     empty_directory name
     empty_directory File.join("#{name}","raw_data")
@@ -25,28 +25,43 @@ class Project < Thor
     empty_directory File.join("#{name}","tasks")
     empty_directory File.join("#{name}","scripts")
     self.name = name # for template to take the correct values
-    template(File.join("..","templates","README.tt"), "#{name}/README.txt")    
     
-    if options[:type] == "annotation"
-        invoke "project:update:annotation", [],{:dir => name}
-    else    
-      empty_directory File.join("#{name}","log")
-      empty_directory File.join("#{name}","conf")
-    end
-  end
-  
-  attr_accessor :type
+    #if options[:type] == "annotation"
+    #    invoke "project:update:annotation", [],{:dir => name}
+    #else    
+    empty_directory File.join("#{name}","log")
+    empty_directory File.join("#{name}","conf") 
+    empty_directory File.join("#{name}","db")
 
-  desc "update [TYPE]", "Update the working dir to a new type of project"
-  method_option :dir, :type => :string
-  def update(type)
-    self.type = type
-    dir = (options[:dir]) ? options[:dir]+"/" : ""
-    empty_directory "#{dir}log"
-    empty_directory "#{dir}conf"
-    empty_directory "#{dir}db"
-    template(File.join("..","templates","db.tt"), "#{dir}conf/#{type}_db.yml")
+		if defined?(JRUBY_VERSION)
+			self.adapter = "jdbcsqlite3"
+		else
+			self.adapter = "sqlite3"
+		end
+		
+		template(File.join("..","templates","db.tt"), "#{name}/conf/database.yml")	
+    template(File.join("..","templates","README.tt"), "#{name}/README.txt")    
+		#end
   end
+ 
+
+#  attr_accessor :type
+#	attr_accessor :adapter
+#  desc "update [TYPE]", "Update the working dir to a new type of project"
+#  method_option :dir, :type => :string
+#  def update(type)
+#    self.type = type
+#		if defined?(JRUBY_VERSION)
+#			self.adapter = "jdbcsqlite3"
+#		else
+#			self.adapter = "sqlite3"
+#		end
+#    dir = (options[:dir]) ? options[:dir]+"/" : ""
+#    empty_directory "#{dir}log"
+#    empty_directory "#{dir}conf"
+#    empty_directory "#{dir}db"
+#    template(File.join("..","templates","db.tt"), "#{dir}conf/#{type}_db.yml")
+#  end
 
   
 end

data/lib/templates/README.tt

@@ -1,6 +1,6 @@
-Copyright (c) 2011 Raoul J.P. Bonnal and Francesco Strozzi.
+Copyright (c) 2012 Raoul J.P. Bonnal and Francesco Strozzi.
 
-Bio-NGS is an official BioRuby Plugin for Next Generation Sequencing data analysis and workflows.
+Bio-NGS is an official BioRuby Gem for Next Generation Sequencing data analysis and workflows.
 
 
 == Description ==
@@ -11,7 +11,9 @@ Here is a tree description:
 
 <%= name %>
  |
- |-- data	# the place to store all your raw data and output files
+ |-- raw_data	# the place to store all your raw data
+ |
+ |-- outputs # the place for analysis results
  |
  |-- log	# the place to store log and temporary files
  |
@@ -40,4 +42,4 @@ Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T.
 
 
 
- 
+ 

data/lib/templates/db.tt

@@ -1,6 +1,6 @@
 # SQLite version 3.x
 #   gem install sqlite3
-adapter: sqlite3
-database: db/<%= type %>.sqlite3
+adapter: <%= adapter  %>
+database: db/<%= name %>.sqlite3
 pool: 5
-timeout: 5000
+timeout: 5000

metadata

@@ -1,8 +1,8 @@
 --- !ruby/object:Gem::Specification
 name: bio-ngs
 version: !ruby/object:Gem::Version
-  version: 0.4.7.alpha.03
-  prerelease: 6
+  version: 0.5.0
+  prerelease: 
 platform: ruby
 authors:
 - Francesco Strozzi
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-29 00:00:00.000000000 Z
+date: 2012-06-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2162360040 !ruby/object:Gem::Requirement
+  requirement: &2153797260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2162360040
+  version_requirements: *2153797260
 - !ruby/object:Gem::Dependency
   name: bio-samtools
-  requirement: &2162358700 !ruby/object:Gem::Requirement
+  requirement: &2153796600 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 0.3.2
   type: :runtime
   prerelease: false
-  version_requirements: *2162358700
+  version_requirements: *2153796600
 - !ruby/object:Gem::Dependency
   name: thor
-  requirement: &2162357760 !ruby/object:Gem::Requirement
+  requirement: &2153795920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - =
@@ -44,10 +44,10 @@ dependencies:
         version: 0.14.6
   type: :runtime
   prerelease: false
-  version_requirements: *2162357760
+  version_requirements: *2153795920
 - !ruby/object:Gem::Dependency
   name: rubyvis
-  requirement: &2162372800 !ruby/object:Gem::Requirement
+  requirement: &2153794440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: 0.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *2162372800
+  version_requirements: *2153794440
 - !ruby/object:Gem::Dependency
   name: daemons
-  requirement: &2162369680 !ruby/object:Gem::Requirement
+  requirement: &2153792480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -66,10 +66,10 @@ dependencies:
         version: 1.1.0
   type: :runtime
   prerelease: false
-  version_requirements: *2162369680
+  version_requirements: *2153792480
 - !ruby/object:Gem::Dependency
   name: ruby-ensembl-api
-  requirement: &2162367460 !ruby/object:Gem::Requirement
+  requirement: &2153791560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -77,10 +77,10 @@ dependencies:
         version: 1.0.1
   type: :runtime
   prerelease: false
-  version_requirements: *2162367460
+  version_requirements: *2153791560
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2162365420 !ruby/object:Gem::Requirement
+  requirement: &2153790500 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,32 +88,10 @@ dependencies:
         version: 3.0.5
   type: :runtime
   prerelease: false
-  version_requirements: *2162365420
-- !ruby/object:Gem::Dependency
-  name: sqlite3
-  requirement: &2162380460 !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.3.3
-  type: :runtime
-  prerelease: false
-  version_requirements: *2162380460
-- !ruby/object:Gem::Dependency
-  name: bio-blastxmlparser
-  requirement: &2162378780 !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: *2162378780
+  version_requirements: *2153790500
 - !ruby/object:Gem::Dependency
   name: progressbar
-  requirement: &2162377060 !ruby/object:Gem::Requirement
+  requirement: &2153805400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -121,10 +99,10 @@ dependencies:
         version: 0.9.0
   type: :runtime
   prerelease: false
-  version_requirements: *2162377060
+  version_requirements: *2153805400
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &2162375820 !ruby/object:Gem::Requirement
+  requirement: &2153804180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - =
@@ -132,10 +110,10 @@ dependencies:
         version: 0.9.2.2
   type: :runtime
   prerelease: false
-  version_requirements: *2162375820
+  version_requirements: *2153804180
 - !ruby/object:Gem::Dependency
   name: json
-  requirement: &2162374160 !ruby/object:Gem::Requirement
+  requirement: &2153802400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -143,10 +121,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2162374160
+  version_requirements: *2153802400
 - !ruby/object:Gem::Dependency
   name: parallel
-  requirement: &2162389180 !ruby/object:Gem::Requirement
+  requirement: &2153800840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -154,10 +132,21 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2162389180
+  version_requirements: *2153800840
+- !ruby/object:Gem::Dependency
+  name: bio-blastxmlparser
+  requirement: &2153800100 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *2153800100
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2162387820 !ruby/object:Gem::Requirement
+  requirement: &2153798900 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -165,10 +154,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2162387820
+  version_requirements: *2153798900
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2162385760 !ruby/object:Gem::Requirement
+  requirement: &2153812960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -176,10 +165,10 @@ dependencies:
         version: 1.1.0
   type: :development
   prerelease: false
-  version_requirements: *2162385760
+  version_requirements: *2153812960
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2162384960 !ruby/object:Gem::Requirement
+  requirement: &2153812040 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -187,10 +176,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *2162384960
+  version_requirements: *2153812040
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2162383380 !ruby/object:Gem::Requirement
+  requirement: &2153811000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -198,10 +187,10 @@ dependencies:
         version: 0.9.11
   type: :development
   prerelease: false
-  version_requirements: *2162383380
+  version_requirements: *2153811000
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2162381840 !ruby/object:Gem::Requirement
+  requirement: &2153809620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -209,10 +198,43 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *2162381840
+  version_requirements: *2153809620
+- !ruby/object:Gem::Dependency
+  name: jdbc-sqlite3
+  requirement: &2153807400 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *2153807400
+- !ruby/object:Gem::Dependency
+  name: activerecord-jdbcsqlite3-adapter
+  requirement: &2153806580 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *2153806580
+- !ruby/object:Gem::Dependency
+  name: sqlite3
+  requirement: &2153821900 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *2153821900
 - !ruby/object:Gem::Dependency
   name: thor
-  requirement: &2162397200 !ruby/object:Gem::Requirement
+  requirement: &2153821100 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - =
@@ -220,10 +242,10 @@ dependencies:
         version: 0.14.6
   type: :development
   prerelease: false
-  version_requirements: *2162397200
+  version_requirements: *2153821100
 - !ruby/object:Gem::Dependency
   name: ffi
-  requirement: &2162394020 !ruby/object:Gem::Requirement
+  requirement: &2153820420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -231,10 +253,10 @@ dependencies:
         version: 1.0.6
   type: :development
   prerelease: false
-  version_requirements: *2162394020
+  version_requirements: *2153820420
 - !ruby/object:Gem::Dependency
   name: rubyvis
-  requirement: &2162392380 !ruby/object:Gem::Requirement
+  requirement: &2153819440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -242,10 +264,10 @@ dependencies:
         version: 0.5.0
   type: :development
   prerelease: false
-  version_requirements: *2162392380
+  version_requirements: *2153819440
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2162391700 !ruby/object:Gem::Requirement
+  requirement: &2153818340 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -253,10 +275,10 @@ dependencies:
         version: 2.5.0
   type: :development
   prerelease: false
-  version_requirements: *2162391700
+  version_requirements: *2153818340
 - !ruby/object:Gem::Dependency
   name: daemons
-  requirement: &2162390160 !ruby/object:Gem::Requirement
+  requirement: &2153816560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -264,10 +286,10 @@ dependencies:
         version: 1.1.0
   type: :development
   prerelease: false
-  version_requirements: *2162390160
+  version_requirements: *2153816560
 - !ruby/object:Gem::Dependency
   name: bio-samtools
-  requirement: &2162405360 !ruby/object:Gem::Requirement
+  requirement: &2153814840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -275,10 +297,10 @@ dependencies:
         version: 0.3.2
   type: :development
   prerelease: false
-  version_requirements: *2162405360
+  version_requirements: *2153814840
 - !ruby/object:Gem::Dependency
   name: ruby-ensembl-api
-  requirement: &2162404740 !ruby/object:Gem::Requirement
+  requirement: &2153827720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -286,10 +308,10 @@ dependencies:
         version: 1.0.1
   type: :development
   prerelease: false
-  version_requirements: *2162404740
+  version_requirements: *2153827720
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2162404160 !ruby/object:Gem::Requirement
+  requirement: &2153826500 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -297,21 +319,21 @@ dependencies:
         version: 3.0.5
   type: :development
   prerelease: false
-  version_requirements: *2162404160
+  version_requirements: *2153826500
 - !ruby/object:Gem::Dependency
-  name: sqlite3
-  requirement: &2162403240 !ruby/object:Gem::Requirement
+  name: progressbar
+  requirement: &2153825440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.3.3
+        version: 0.9.0
   type: :development
   prerelease: false
-  version_requirements: *2162403240
+  version_requirements: *2153825440
 - !ruby/object:Gem::Dependency
-  name: bio-blastxmlparser
-  requirement: &2162401800 !ruby/object:Gem::Requirement
+  name: json
+  requirement: &2153824660 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -319,21 +341,21 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2162401800
+  version_requirements: *2153824660
 - !ruby/object:Gem::Dependency
-  name: progressbar
-  requirement: &2162399920 !ruby/object:Gem::Requirement
+  name: rake
+  requirement: &2153823940 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - =
       - !ruby/object:Gem::Version
-        version: 0.9.0
+        version: 0.9.2.2
   type: :development
   prerelease: false
-  version_requirements: *2162399920
+  version_requirements: *2153823940
 - !ruby/object:Gem::Dependency
-  name: json
-  requirement: &2162413940 !ruby/object:Gem::Requirement
+  name: parallel
+  requirement: &2153823140 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -341,21 +363,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2162413940
+  version_requirements: *2153823140
 - !ruby/object:Gem::Dependency
-  name: rake
-  requirement: &2162412560 !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - =
-      - !ruby/object:Gem::Version
-        version: 0.9.2.2
-  type: :development
-  prerelease: false
-  version_requirements: *2162412560
-- !ruby/object:Gem::Dependency
-  name: parallel
-  requirement: &2162411560 !ruby/object:Gem::Requirement
+  name: bio-blastxmlparser
+  requirement: &2153822560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -363,7 +374,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2162411560
+  version_requirements: *2153822560
 description: bio-ngs provides a framework for handling NGS data with BioRuby
 email: francesco.strozzi@gmail.com
 executables:
@@ -372,13 +383,13 @@ extensions:
 - ext/mkrf_conf.rb
 extra_rdoc_files:
 - LICENSE.txt
-- README.rdoc
+- README.md
 files:
 - .document
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
-- README.rdoc
+- README.md
 - Rakefile
 - VERSION
 - bin/biongs
@@ -389,6 +400,7 @@ files:
 - features/illumina_project_rebuild.feature
 - features/step_definitions/cufflinks_gtf.rb
 - features/step_definitions/cufflinks_gtf_parser_indexing.rb
+- features/step_definitions/illumina_project_rebuild.rb
 - features/support/env.rb
 - lib/bio-ngs.rb
 - lib/bio/appl/ngs/bcftools.rb
@@ -433,7 +445,6 @@ files:
 - lib/bio/ngs/record.rb
 - lib/bio/ngs/task.rb
 - lib/bio/ngs/utils.rb
-- lib/development_tasks.rb
 - lib/enumerable.rb
 - lib/meta.rb
 - lib/tasks/bwa.thor
@@ -441,6 +452,7 @@ files:
 - lib/tasks/filter.thor
 - lib/tasks/history.thor
 - lib/tasks/homology.thor
+- lib/tasks/install.thor
 - lib/tasks/ontology.thor
 - lib/tasks/pre.thor
 - lib/tasks/project.thor
@@ -553,13 +565,13 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -803718584135061941
+      hash: 330803756225747013
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
-  - - ! '>'
+  - - ! '>='
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.10