genomer 0.0.7 → 0.0.8

data/Gemfile

@@ -1,4 +1,2 @@
 source :rubygems
 gemspec
-
-gem "md2man", :git => "git://github.com/sunaku/md2man.git", :ref => "c87dab11"

data/README.mkd

@@ -0,0 +1,59 @@
+![Genomer: A swiss army knife for genome projects](http://genomer.s3.amazonaws.com/icon/genomer.png)
+
+## About
+
+Genomer is command line glue for genome projects. I wrote this tool to simplify
+the small but tedious tasks required when finishing a genome. Genomer does not
+perform assembly, gap closing or genome annotation. Genomer does however make
+it easy to reorganise contigs in a genome, map annotations on to the genome and
+generate the files required to submit a genome.
+
+A important part of genomer is making all projects reproducible. Genomer is
+designed to work well with build tools such as [GNU Make][make] and revision
+control tools such as [git][git]. This allows for all steps taken in genome
+project to be tracked and reverted if required.
+
+[make]: http://www.gnu.org/software/make/
+[git]: http://git-scm.com/
+
+Genomer is also built as a modular tool where additional functions are added by
+installing plugins. Plugins can be added simply by naming them in the `Gemfile`
+in the genomer project root, followed typing the command `bundle install`.
+Furthermore plugins can be specified to specific versions, this means that new
+versions of genomer plugins will not break any existing genomer projects.
+
+## Examples
+
+I wrote genomer to simplify the manual and error prone tasks in my own genome
+projects. You can see examples of using genomer for [a small plasmid][plasmid]
+and for [a larger microbial genome][genome]. Each of these projects takes
+advantage of revision control and build files to make the projects
+reproducible.
+
+[plasmid]: https://github.com/michaelbarton/chromosome-pfluorescens-r124-plasmid
+[genome]: https://github.com/michaelbarton/chromosome-pfluorescens-r124-genome
+
+## Installing
+
+Ruby and RubyGems are required to use genomer and related plugins. Genomer is
+installed on the command line using:
+
+    $ gem install genomer
+
+## Contact
+
+Genomer is developed by Michael Barton (www.michaelbarton.me.uk). The source
+code is available on [github][]. Bug reports and feature requests should also
+be made there.
+
+[github]: https://github.com/michaelbarton/genomer
+
+## Copyright
+
+Genomer copyright (c) 2010 by Michael Barton. Genomer is licensed under the MIT
+license. See LICENSE.txt for further details. The swiss army knife image is by
+[Alan Cann][cann] used under a Creative Commons Attribution Non-Commercial
+ShareAlike 2.0 Licence. The original can be [found on flickr.][flickr]
+
+[cann]: http://microbiologybytes.com/AJC/
+[flickr]: http://www.flickr.com/photos/ajc1/4663140532/

data/features/cli/init.feature

@@ -6,6 +6,11 @@ Feature: Creating a new genomer project
   Scenario: Creating a new project
     When I run the genomer command with the arguments "init project"
     Then the exit status should be 0
+     And the stdout should contain:
+     """
+     Genomer project 'project' created.
+
+     """
     And a directory named "project" should exist
     And a directory named "project/assembly" should exist
     And a file named "project/assembly/scaffold.yml" should exist
@@ -67,3 +72,12 @@ Feature: Creating a new genomer project
      """
      The scaffold contains 1 entries
      """
+
+   Scenario: Creating a new project where the directory already exists
+     Given a directory named "project"
+     When I run the genomer command with the arguments "init project"
+     Then the exit status should be 1
+     And the stderr should contain:
+     """
+     Error. Directory 'project' already exists.
+     """

data/features/cli/man.feature

@@ -69,3 +69,9 @@ Feature: Showing man pages for available commands
       Error. No manual entry for command 'simple unknown'
 
       """
+
+  @disable-bundler
+  Scenario: Getting the man page for init
+     When I run the genomer command with the arguments "man init"
+     Then the exit status should be 0
+      And the output should contain "GENOMER-INIT(1)"

data/genomer.gemspec

@@ -16,12 +16,12 @@ Gem::Specification.new do |s|
   s.rubyforge_project         = "genomer"
 
   s.add_dependency "rake",                          "~> 0.9.0"
-  s.add_dependency "bundler",                       "~> 1.1.0"
+  s.add_dependency "bundler",                        "> 1.1.0"
   s.add_dependency "configliere",                   "~> 0.4.8"
   s.add_dependency "scaffolder",                    "~> 0.4.0"
   s.add_dependency "scaffolder-annotation-locator", ">= 0.1.4"
   s.add_dependency "unindent",                      "~> 1.0.0"
-  s.add_dependency "md2man",                        "~> 1.2.0"
+  s.add_dependency "md2man",                        "~> 1.4.0"
 
   # Specs
   s.add_development_dependency "rspec",                   "~> 2.7.0"

data/lib/genomer/runtime.rb

@@ -53,12 +53,17 @@ class Genomer::Runtime
 
   def man
     if not arguments.empty?
-      man_file_location = man_file(arguments.clone)
-      unless File.exists?(man_file_location)
+      location = if arguments.first == 'init'
+                   File.expand_path File.dirname(__FILE__) + '/../../man/genomer-init.1.ronn'
+                 else
+                   man_file(arguments.clone)
+                 end
+
+      unless File.exists?(location)
         raise Genomer::Error, "No manual entry for command '#{arguments.join(' ')}'"
       end
 
-      Kernel.exec "man #{groffed_man_file(man_file_location).path}"
+      Kernel.exec "man #{groffed_man_file(location).path}"
     else
       msg =<<-EOF
         genomer man COMMAND
@@ -94,7 +99,6 @@ class Genomer::Runtime
     Dir.mkdir project_name
     Dir.mkdir File.join(project_name,'assembly')
 
-
     File.open(File.join(project_name,'Gemfile'),'w') do |file|
       file.print Genomer::Files.gemfile
     end
@@ -104,6 +108,9 @@ class Genomer::Runtime
         file.print Genomer::Files.send(name.gsub('.','_').to_sym)
       end
     end
+
+    "Genomer project '#{project_name}' created.\n"
+
   end
 
   def run_plugin

data/lib/genomer/version.rb

@@ -1,3 +1,3 @@
 module Genomer
-  VERSION = "0.0.7"
+  VERSION = "0.0.8"
 end

data/man/genomer-init.1.ronn

@@ -11,7 +11,35 @@ genomer-init(1) -- create a new genomer project
 ## DESCRIPTION
 
 Creates a new genomer project directory named **project-name**. Returns an
-error if the project directory already exists.
+error if the project directory already exists. This created directory has the
+following structure. Each file is described below.
+
+    **project-name**
+    ├── Gemfile
+    └── assembly
+        ├── annotations.gff
+        ├── scaffold.yml
+        └── sequence.fna
+
+* **Gemfile**: Genomer plugins are specified here. After adding a plugin the
+  command `bundle install` should run to install the required plugins. Gems are
+  specified according to [the bundler documentation][bundler]. Each plugin
+  should begin with the suffix 'genomer-plugin.'
+
+* **sequence.fna**: The file containing your contigs and scaffolds. These
+  should be stored in fasta format.
+
+* **scaffold.yml**: The specifies the final layout of your genome. The scaffold
+  file is written the YAML format. Details and examples of the scaffold format
+  can be found on the [next.gs][] website.
+
+* **annotations.gff**: Specific your genome annotations in [gff3 format][gff]
+  here. The **seqid** column should match the corresponding name of the fasta
+  sequence in the **sequence.fna** file.
+
+[bundler]: http://gembundler.com/
+[gff]: http://www.sequenceontology.org/gff3.shtml
+[next.gs]: http://next.gs
 
 ## BUGS
 

data/spec/genomer/runtime_spec.rb

@@ -49,7 +49,11 @@ describe Genomer::Runtime do
       describe "with project name argument" do
 
         before do
-          subject.execute!
+          @msg = subject.execute!
+        end
+
+        it "should print message that project has been created" do
+          @msg.should == "Genomer project 'project_name' created.\n"
         end
 
         it "should create a directory from the named argument" do
@@ -133,12 +137,12 @@ describe Genomer::Runtime do
 
     describe "help" do
 
-      let(:arguments){ %w|help| }
-
       before do
         mock(Genomer::Plugin).plugins{ gems }
       end
 
+      let(:arguments){ %w|help| }
+
       describe "with no available plugins" do
 
         let(:gems) do
@@ -186,7 +190,7 @@ describe Genomer::Runtime do
         stub(Genomer::Plugin).plugins{ gems }
       end
 
-      describe "with no command specified" do
+      describe "and no command specified" do
 
         let(:arguments){ %w|man| }
 
@@ -200,7 +204,7 @@ describe Genomer::Runtime do
 
       end
 
-      describe "with a command specified" do
+      describe "and a command specified" do
 
         let(:arguments){ %w|man simple| }
         let(:man_file){ 'a' }
@@ -219,6 +223,25 @@ describe Genomer::Runtime do
 
       end
 
+      describe "and the init command specified" do
+
+        let(:arguments){ %w|man init| }
+        let(:man_file){ File.expand_path File.dirname(__FILE__) + '/../../man/genomer-init.1.ronn' }
+        let(:groffed_man_file){ mock!.path{ 'b' } }
+
+        before do
+          dont_allow(subject).man_file
+          mock(subject).groffed_man_file(man_file){ groffed_man_file }
+          mock(File).exists?(man_file){true}
+        end
+
+        it "should call man for the groffed path" do
+          mock(Kernel).exec("man b")
+          subject.execute!
+        end
+
+      end
+
       describe "with a subcommand specified" do
 
         let(:arguments){ %w|man simple subcommand| }

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genomer
 version: !ruby/object:Gem::Version
-  version: 0.0.7
+  version: 0.0.8
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-06-06 00:00:00.000000000 Z
+date: 2013-01-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -32,7 +32,7 @@ dependencies:
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>'
       - !ruby/object:Gem::Version
         version: 1.1.0
   type: :runtime
@@ -40,7 +40,7 @@ dependencies:
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>'
       - !ruby/object:Gem::Version
         version: 1.1.0
 - !ruby/object:Gem::Dependency
@@ -114,7 +114,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.2.0
+        version: 1.4.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -122,7 +122,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.2.0
+        version: 1.4.0
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -232,10 +232,9 @@ files:
 - .travis.yml
 - Gemfile
 - LICENSE.txt
-- README.rdoc
+- README.mkd
 - Rakefile
 - bin/genomer
-- cucumber.yml
 - features/api/annotation_ids.feature
 - features/api/annotation_location.feature
 - features/cli/error.feature
@@ -275,7 +274,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -2433583334421431310
+      hash: -1310621877616390557
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:

data/README.rdoc

@@ -1,23 +0,0 @@
-== Synopsis
-
-Genomer is a plugin-based framework for genome finishing. Plugins are installed
-using the RubyGems package management system. Genome files are managed as a
-directory and updated at the command line using the `genomer` command.
-
-== Installing
-
-Ruby and RubyGems are required to use genomer and related plugins. Genomer is
-installed on the command line using:
-
-  $ gem install genomer
-
-== Contact
-
-Genomer is developed by Michael Barton (www.michaelbarton.me.uk). The source
-code is available on github. Bug reports and feature requests should also be
-made there.
-
-== Copyright
-
-Genomer copyright (c) 2010 by Michael Barton. Scaffolder is licensed under the
-MIT license. See LICENSE.txt for further details.

data/cucumber.yml

@@ -1,2 +0,0 @@
----
-  default: --format progress --color