genfrag 0.0.0.1

data/tasks/svn.rake

@@ -0,0 +1,47 @@
+
+if HAVE_SVN
+
+unless PROJ.svn.root
+  info = %x/svn info ./
+  m = %r/^Repository Root:\s+(.*)$/.match(info)
+  PROJ.svn.root = (m.nil? ? '' : m[1])
+end
+PROJ.svn.root = File.join(PROJ.svn.root, PROJ.svn.path) unless PROJ.svn.path.empty?
+
+namespace :svn do
+
+  # A prerequisites task that all other tasks depend upon
+  task :prereqs
+
+  desc 'Show tags from the SVN repository'
+  task :show_tags => 'svn:prereqs' do |t|
+    tags = %x/svn list #{File.join(PROJ.svn.root, PROJ.svn.tags)}/
+    tags.gsub!(%r/\/$/, '')
+    tags = tags.split("\n").sort {|a,b| b <=> a}
+    puts tags
+  end
+
+  desc 'Create a new tag in the SVN repository'
+  task :create_tag => 'svn:prereqs' do |t|
+    v = ENV['VERSION'] or abort 'Must supply VERSION=x.y.z'
+    abort "Versions don't match #{v} vs #{PROJ.version}" if v != PROJ.version
+
+    svn = PROJ.svn
+    trunk = File.join(svn.root, svn.trunk)
+    tag = "%s-%s" % [PROJ.name, PROJ.version]
+    tag = File.join(svn.root, svn.tags, tag)
+    msg = "Creating tag for #{PROJ.name} version #{PROJ.version}"
+
+    puts "Creating SVN tag '#{tag}'"
+    unless system "svn cp -m '#{msg}' #{trunk} #{tag}"
+      abort "Tag creation failed" 
+    end
+  end
+
+end  # namespace :svn
+
+task 'gem:release' => 'svn:create_tag'
+
+end  # if PROJ.svn.path
+
+# EOF

data/tasks/test.rake

@@ -0,0 +1,40 @@
+
+if test(?e, PROJ.test.file) or not PROJ.test.files.to_a.empty?
+require 'rake/testtask'
+
+namespace :test do
+
+  Rake::TestTask.new(:run) do |t|
+    t.libs = PROJ.libs
+    t.test_files = if test(?f, PROJ.test.file) then [PROJ.test.file]
+                   else PROJ.test.files end
+    t.ruby_opts += PROJ.ruby_opts
+    t.ruby_opts += PROJ.test.opts
+  end
+
+  if HAVE_RCOV
+    desc 'Run rcov on the unit tests'
+    task :rcov => :clobber_rcov do
+      opts = PROJ.rcov.opts.dup << '-o' << PROJ.rcov.dir
+      opts = opts.join(' ')
+      files = if test(?f, PROJ.test.file) then [PROJ.test.file]
+              else PROJ.test.files end
+      files = files.join(' ')
+      sh "#{RCOV} #{files} #{opts}"
+    end
+
+    task :clobber_rcov do
+      rm_r 'coverage' rescue nil
+    end
+  end
+
+end  # namespace :test
+
+desc 'Alias to test:run'
+task :test => 'test:run'
+
+task :clobber => 'test:clobber_rcov' if HAVE_RCOV
+
+end
+
+# EOF

metadata

@@ -0,0 +1,136 @@
+--- !ruby/object:Gem::Specification 
+name: genfrag
+version: !ruby/object:Gem::Version 
+  version: 0.0.0.1
+platform: ruby
+authors: 
+- Pjotr Prins and Trevor Wennblom
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2009-02-26 00:00:00 -06:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: bioruby
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: rake
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.8.3
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: bones
+  type: :development
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 2.4.0
+    version: 
+description: This is a development release. Few features are functional at this time.  Genfrag allows for rapid in-silico searching of fragments cut by different restriction enzymes in large nucleotide acid databases, followed by matching specificity adapters which allow a further data reduction when looking for differential expression of genes and markers.
+email: trevor@corevx.com
+executables: 
+- genfrag
+extensions: []
+
+extra_rdoc_files: 
+- History.txt
+- LICENSE.txt
+- README.rdoc
+- bin/genfrag
+files: 
+- .bnsignore
+- History.txt
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- bin/genfrag
+- lib/genfrag.rb
+- lib/genfrag/app.rb
+- lib/genfrag/app/command.rb
+- lib/genfrag/app/index_command.rb
+- lib/genfrag/app/index_command/db.rb
+- lib/genfrag/app/search_command.rb
+- lib/genfrag/app/search_command/match.rb
+- lib/genfrag/app/search_command/process_file.rb
+- lib/genfrag/app/search_command/trim.rb
+- lib/genfrag/debug.rb
+- spec/data/index_command/in/a.fasta
+- spec/data/index_command/out/1-a_lookup.tdf
+- spec/data/index_command/out/2-a_lookup.db
+- spec/data/index_command/out/3-a_lookup.tdf
+- spec/data/index_command/out/4-a_lookup.db
+- spec/data/index_command/out/5-a_lookup.tdf
+- spec/data/index_command/out/6-a_lookup.db
+- spec/data/index_command/out/a.fasta.db
+- spec/data/index_command/out/a.fasta.tdf
+- spec/genfrag/app/command_spec.rb
+- spec/genfrag/app/index_command_spec.rb
+- spec/genfrag/app/search_command/match_spec.rb
+- spec/genfrag/app/search_command/process_file_spec.rb
+- spec/genfrag/app/search_command/trim_spec.rb
+- spec/genfrag/app/search_command_spec.rb
+- spec/genfrag/app_spec.rb
+- spec/genfrag_spec.rb
+- spec/spec_helper.rb
+- tasks/ann.rake
+- tasks/bones.rake
+- tasks/gem.rake
+- tasks/git.rake
+- tasks/notes.rake
+- tasks/post_load.rake
+- tasks/rdoc.rake
+- tasks/rubyforge.rake
+- tasks/setup.rb
+- tasks/spec.rake
+- tasks/svn.rake
+- tasks/test.rake
+has_rdoc: true
+homepage: http://genfrag.rubyforge.org
+post_install_message: |
+  --------------------------------------------
+   Genfrag installed
+     Type 'genfrag -h' for a list of commands
+  --------------------------------------------
+
+rdoc_options: 
+- --main
+- README.rdoc
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: genfrag
+rubygems_version: 1.3.1
+signing_key: 
+specification_version: 2
+summary: This is a development release
+test_files: []
+