transrate 1.0.0 → 1.0.1

data/test/vagrant/fedora_20_64/provision.sh

@@ -0,0 +1,16 @@
+# Setup
+sudo yum install curl
+
+# Install a multi-user RVM install with the latest ruby`
+\curl -sSL https://get.rvm.io | sudo bash -s stable --ruby
+source /etc/profile.d/rvm.sh
+
+  # Add user to RVM group
+sudo usermod -a -G rvm vagrant
+su vagrant
+
+# Install transrate
+gem install transrate --pre
+
+# Install dependencies
+transrate --install-deps

data/test/vagrant/linux-x86_64/Vagrantfile

@@ -0,0 +1,10 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+# Vagrantfile API/syntax version. Don't touch unless you know what you're doing!
+VAGRANTFILE_API_VERSION = "2"
+
+Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
+  config.vm.box = "andy_b_84/debian-squeeze64-vanilla"
+  config.vm.network :forwarded_port, guest: 22, host: 18723
+end

data/test/vagrant/osx/Vagrantfile

@@ -0,0 +1,18 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+# Vagrantfile API/syntax version. Don't touch unless you know what you're doing!
+VAGRANTFILE_API_VERSION = "2"
+
+Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
+  # Every Vagrant virtual environment requires a box to build off of.
+  config.vm.box = "http://files.dryga.com/boxes/osx-yosemite-0.2.0.box"
+
+  # config.vm.synced_folder "../data", "/vagrant_data"
+  config.vm.provider "virtualbox" do |vb|
+    config.vm.synced_folder ".", "/vagrant", type: "nfs"
+  end
+
+  config.vm.provision "shell", path: "../../../packaging/build_deps_macosx.sh"
+
+end

data/test/vagrant/ubuntu_12.04_64/Vagrantfile

@@ -0,0 +1,126 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+# Vagrantfile API/syntax version. Don't touch unless you know what you're doing!
+VAGRANTFILE_API_VERSION = "2"
+
+Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
+  # All Vagrant configuration is done here. The most common configuration
+  # options are documented and commented below. For a complete reference,
+  # please see the online documentation at vagrantup.com.
+
+  # Every Vagrant virtual environment requires a box to build off of.
+  config.vm.box = "hashicorp/precise64"
+
+  # Provision the virtual machine with a local script, provision.sh,
+  # in the same directory as the Vagrantfile
+  config.vm.provision "shell", path: "provision.sh"
+
+  # Disable automatic box update checking. If you disable this, then
+  # boxes will only be checked for updates when the user runs
+  # `vagrant box outdated`. This is not recommended.
+  # config.vm.box_check_update = false
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine. In the example below,
+  # accessing "localhost:8080" will access port 80 on the guest machine.
+  # config.vm.network "forwarded_port", guest: 80, host: 8080
+
+  # Create a private network, which allows host-only access to the machine
+  # using a specific IP.
+  # config.vm.network "private_network", ip: "192.168.33.10"
+
+  # Create a public network, which generally matched to bridged network.
+  # Bridged networks make the machine appear as another physical device on
+  # your network.
+  # config.vm.network "public_network"
+
+  # If true, then any SSH connections made will enable agent forwarding.
+  # Default value: false
+  # config.ssh.forward_agent = true
+
+  # Share an additional folder to the guest VM. The first argument is
+  # the path on the host to the actual folder. The second argument is
+  # the path on the guest to mount the folder. And the optional third
+  # argument is a set of non-required options.
+  # config.vm.synced_folder "../data", "/vagrant_data"
+
+  # Provider-specific configuration so you can fine-tune various
+  # backing providers for Vagrant. These expose provider-specific options.
+  # Example for VirtualBox:
+  #
+  # config.vm.provider "virtualbox" do |vb|
+  #   # Don't boot with headless mode
+  #   vb.gui = true
+  #
+  #   # Use VBoxManage to customize the VM. For example to change memory:
+  #   vb.customize ["modifyvm", :id, "--memory", "1024"]
+  # end
+  #
+  # View the documentation for the provider you're using for more
+  # information on available options.
+
+  # Enable provisioning with CFEngine. CFEngine Community packages are
+  # automatically installed. For example, configure the host as a
+  # policy server and optionally a policy file to run:
+  #
+  # config.vm.provision "cfengine" do |cf|
+  #   cf.am_policy_hub = true
+  #   # cf.run_file = "motd.cf"
+  # end
+  #
+  # You can also configure and bootstrap a client to an existing
+  # policy server:
+  #
+  # config.vm.provision "cfengine" do |cf|
+  #   cf.policy_server_address = "10.0.2.15"
+  # end
+
+  # Enable provisioning with Puppet stand alone.  Puppet manifests
+  # are contained in a directory path relative to this Vagrantfile.
+  # You will need to create the manifests directory and a manifest in
+  # the file default.pp in the manifests_path directory.
+  #
+  # config.vm.provision "puppet" do |puppet|
+  #   puppet.manifests_path = "manifests"
+  #   puppet.manifest_file  = "site.pp"
+  # end
+
+  # Enable provisioning with chef solo, specifying a cookbooks path, roles
+  # path, and data_bags path (all relative to this Vagrantfile), and adding
+  # some recipes and/or roles.
+  #
+  # config.vm.provision "chef_solo" do |chef|
+  #   chef.cookbooks_path = "../my-recipes/cookbooks"
+  #   chef.roles_path = "../my-recipes/roles"
+  #   chef.data_bags_path = "../my-recipes/data_bags"
+  #   chef.add_recipe "mysql"
+  #   chef.add_role "web"
+  #
+  #   # You may also specify custom JSON attributes:
+  #   chef.json = { mysql_password: "foo" }
+  # end
+
+  # Enable provisioning with chef server, specifying the chef server URL,
+  # and the path to the validation key (relative to this Vagrantfile).
+  #
+  # The Opscode Platform uses HTTPS. Substitute your organization for
+  # ORGNAME in the URL and validation key.
+  #
+  # If you have your own Chef Server, use the appropriate URL, which may be
+  # HTTP instead of HTTPS depending on your configuration. Also change the
+  # validation key to validation.pem.
+  #
+  # config.vm.provision "chef_client" do |chef|
+  #   chef.chef_server_url = "https://api.opscode.com/organizations/ORGNAME"
+  #   chef.validation_key_path = "ORGNAME-validator.pem"
+  # end
+  #
+  # If you're using the Opscode platform, your validator client is
+  # ORGNAME-validator, replacing ORGNAME with your organization name.
+  #
+  # If you have your own Chef Server, the default validation client name is
+  # chef-validator, unless you changed the configuration.
+  #
+  #   chef.validation_client_name = "ORGNAME-validator"
+end

data/test/vagrant/ubuntu_12.04_64/provision.sh

@@ -0,0 +1,24 @@
+su vagrant
+
+# Setup
+sudo apt-get update -y
+sudo apt-get install -y curl build-essential git
+
+# Install a multi-user RVM install with the latest ruby
+sudo gpg --keyserver hkp://keys.gnupg.net --recv-keys D39DC0E3
+\curl -sSL https://get.rvm.io | bash -s stable --ruby
+source /usr/local/rvm/scripts/rvm
+
+# Add user to RVM group
+sudo usermod -a -G rvm vagrant
+
+# Install transrate
+git clone https://github.com/Blahah/transrate.git
+cd transrate
+sudo chmod -R 777 .
+
+# Install dependencies
+gem install bundler rake
+bundle install
+bundle exec rake compile
+bundle exec bin/transrate --install-deps

data/transrate.gemspec

@@ -28,8 +28,8 @@ Gem::Specification.new do |gem|
   gem.add_development_dependency 'test-unit', '~> 3.0'
   gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
   gem.add_development_dependency 'rake-compiler', '~> 0.9', '>= 0.9.2'
-  gem.add_development_dependency 'turn', '~> 0.9', '>= 0.9.7'
-  gem.add_development_dependency 'minitest', '~> 4', '>= 4.7.5'
+  gem.add_development_dependency 'minitest', '~> 5'
+  gem.add_development_dependency 'minitest-reporters', '~> 1', '>= 1.0.17'
   gem.add_development_dependency 'simplecov', '~> 0.8', '>= 0.8.2'
   gem.add_development_dependency 'shoulda', '~> 3.5', '>= 3.5.0'
   gem.add_development_dependency 'coveralls', '~> 0.7', '>= 0.7.2'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: transrate
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.0.1
 platform: ruby
 authors:
 - Richard Smith-Unna
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-06-15 00:00:00.000000000 Z
+date: 2015-07-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: yell
@@ -209,45 +209,39 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 0.9.2
 - !ruby/object:Gem::Dependency
-  name: turn
+  name: minitest
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.9'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.9.7
+        version: '5'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.9'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.9.7
+        version: '5'
 - !ruby/object:Gem::Dependency
-  name: minitest
+  name: minitest-reporters
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4'
+        version: '1'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.7.5
+        version: 1.0.17
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4'
+        version: '1'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.7.5
+        version: 1.0.17
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
@@ -318,6 +312,7 @@ extensions:
 extra_rdoc_files: []
 files:
 - ".gitignore"
+- ".travis.yml"
 - CITATION
 - Gemfile
 - LICENSE
@@ -326,11 +321,14 @@ files:
 - bin/transrate
 - deps/blast.yaml
 - deps/deps.yaml
+- docs/transrate_logo_full.png
 - ext/transrate/extconf.rb
 - ext/transrate/transrate.c
+- files.txt
 - lib/transrate.rb
 - lib/transrate/assembly.rb
 - lib/transrate/cmd.rb
+- lib/transrate/cmdline.rb
 - lib/transrate/comparative_metrics.rb
 - lib/transrate/contig.rb
 - lib/transrate/contig_metrics.rb
@@ -341,6 +339,11 @@ files:
 - lib/transrate/transrater.rb
 - lib/transrate/version.rb
 - lib/transrate/writer.rb
+- packaging/build_deps_linux.sh
+- packaging/build_deps_macosx.sh
+- packaging/bundler-config
+- packaging/minify.sh
+- packaging/transrate
 - test/data/150uncovered.l.fq
 - test/data/150uncovered.r.fq
 - test/data/Os.protein.2.fa
@@ -352,11 +355,20 @@ files:
 - test/data/sorghum_100.fa
 - test/data/sorghum_transcript.fa
 - test/data/test.sf
+- test/data/test_contig_nc1.fa
+- test/data/test_contig_nc2.fa
+- test/data/test_contig_nc3.fa
+- test/data/test_contig_nc4.fa
+- test/data/test_contig_nc5.fa
+- test/data/test_contig_nc6.fa
+- test/data/test_contig_nc7.fa
+- test/data/test_reference_aa1.fa
+- test/data/test_reference_nc1.fa
 - test/data/tiny.sam
 - test/helper.rb
 - test/test_assembly.rb
-- test/test_bin.rb
 - test/test_cmd.rb
+- test/test_cmdline.rb
 - test/test_comp_metrics.rb
 - test/test_contig.rb
 - test/test_contig_metrics.rb
@@ -367,6 +379,15 @@ files:
 - test/test_snap.rb
 - test/test_transrate.rb
 - test/test_transrater.rb
+- test/vagrant/centos_6.5_64/Vagrantfile
+- test/vagrant/debian_7.4_64/Vagrantfile
+- test/vagrant/debian_7.4_64/provision.sh
+- test/vagrant/fedora_20_64/Vagrantfile
+- test/vagrant/fedora_20_64/provision.sh
+- test/vagrant/linux-x86_64/Vagrantfile
+- test/vagrant/osx/Vagrantfile
+- test/vagrant/ubuntu_12.04_64/Vagrantfile
+- test/vagrant/ubuntu_12.04_64/provision.sh
 - transrate.gemspec
 homepage: https://github.com/Blahah/transrate
 licenses:

data/test/test_bin.rb

@@ -1,139 +0,0 @@
-require 'helper'
-require 'csv'
-
-class TestTransrateBin < Test::Unit::TestCase
-
-  context "Transrate" do
-
-    setup do
-
-    end
-
-    teardown do
-      files = ["sorghum_100.1.fastq.sorghum_100.2.fastq.sorghum_100.bam.bai",
-      "sorghum_100.1.fastq.sorghum_100.2.fastq.sorghum_100.bam",
-      "sorghum_100_into_Os.protein.2.1.blast",
-      "assembly.2_into_Os.protein.2.1.blast",
-      "sorghum_100.nhr", "sorghum_100.nin", "sorghum_100.nsq",
-      "Os.protein.2_into_sorghum_100.2.blast",
-      "Os.protein.2_into_assembly.2.2.blast",
-      "assembly.2.nhr",  "assembly.2.nin",  "assembly.2.nsq",
-      "Os.protein.2.phr",  "Os.protein.2.pin",  "Os.protein.2.psq",
-      "transrate_assemblies.csv",
-      "sorghum_100.fa_quant.sf",
-      "sorghum_100.fa_bam_info.csv",
-      "transrate_sorghum_100.fa_contigs.csv",
-      "sorghum_100.1.fastq-sorghum_100.2.fastq-read_count.txt",
-      "sorghum_100.1.fastq.sorghum_100.2.fastq.sorghum_100.assigned.bam",
-      "bad.sorghum_100.fa", "chimeric.sorghum_100.fa",
-      "fragmented.sorghum_100.fa", "good.sorghum_100.fa"]
-      files.each do |file|
-        File.delete(file) if File.exist?(file)
-      end
-      `rm -rf sorghum_100`
-      `rm -rf logs`
-      `rm -rf libParams`
-    end
-
-    should "run help" do
-      c=Transrate::Cmd.new("bundle exec bin/transrate --help")
-      c.run
-      assert c.stdout =~ /DESCRIPTION/
-      assert_equal true, c.status.success?, "exit status"
-    end
-
-    should "fail on non existent assembly files" do
-      c=Transrate::Cmd.new("bundle exec bin/transrate --assembly foo.fasta")
-      c.run
-      assert_equal false, c.status.success?, "exit success"
-    end
-
-    should "fail on non existent reference files" do
-      c=Transrate::Cmd.new("bundle exec bin/transrate --reference foo.fasta")
-      c.run
-      assert_equal false, c.status.success?, "exit status"
-    end
-
-    should "run on test data" do
-      assembly = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.fa')
-      reference = File.join(File.dirname(__FILE__), 'data', 'Os.protein.2.fa')
-      left = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.1.fastq')
-      right = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.2.fastq')
-      cmd = "bundle exec bin/transrate --assembly #{assembly}"
-      cmd << " --reference #{reference}"
-      cmd << " --left #{left}"
-      cmd << " --right #{right}"
-      c = Transrate::Cmd.new("#{cmd}")
-      c.run
-      assert_equal true, c.status.success?, "exit status"
-      assert File.exist?("transrate_assemblies.csv"), "csv file doesn't exist"
-      assert File.exist?("transrate_sorghum_100.fa_contigs.csv"),
-             "contig csv file doesn't exist"
-      hash = {}
-      CSV.foreach("transrate_assemblies.csv", :headers => true,
-                                   :header_converters => :symbol,
-                                   :converters => :all) do |row|
-        row.headers
-        row.fields
-        row.headers.zip(row.fields).each do |header, field|
-          hash[header]=field
-        end
-      end
-      assert_in_delta 137748, hash[:n_bases], 1000, "number of bases"
-      assert_equal 1692, hash[:n50], "n50"
-      assert_equal 2, hash[:n_refs_with_crbb], "number of crb hits"
-      assert_equal 2, hash[:n_contigs_with_crbb], "number of contigs with hits"
-    end
-
-    should "run on test data with comma separated list of fastq files" do
-      assembly = File.join(File.dirname(__FILE__), 'data', 'sorghum_100.fa')
-      left = []
-      right = []
-      left << File.join(File.dirname(__FILE__), 'data', 'sorghum_100.1.fastq')
-      left << File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
-      right << File.join(File.dirname(__FILE__), 'data', 'sorghum_100.2.fastq')
-      right << File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
-      cmd = "bundle exec bin/transrate --assembly #{assembly}"
-      cmd << " --left #{left.join(",")}"
-      cmd << " --right #{right.join(",")}"
-      c = Transrate::Cmd.new("#{cmd}")
-      c.run
-      if !(c.status.success?)
-        puts c.stdout
-        puts c.stderr
-      end
-      assert_equal true, c.status.success?, "exit status"
-      assert File.exist?("transrate_assemblies.csv")
-      assert File.exist?("transrate_sorghum_100.fa_contigs.csv"),
-             "contig csv file doesn't exist"
-      hash = {}
-      CSV.foreach("transrate_assemblies.csv", :headers => true,
-                                   :header_converters => :symbol,
-                                   :converters => :all) do |row|
-        row.headers.zip(row.fields).each do |header, field|
-          hash[header]=field
-        end
-      end
-      assert_in_delta 137748, hash[:n_bases], 1000, "number of bases"
-      assert_equal 1692, hash[:n50], "n50"
-      assert_equal 25006 + 223, hash[:fragments], "number of reads"
-    end
-
-    should "fail when one of multiple assemblies is missing" do
-      assembly = File.join(File.dirname(__FILE__), 'data', 'assembly.2.fa')
-      assembly2 = File.join(File.dirname(__FILE__), 'data', 'foo.fa')
-      reference = File.join(File.dirname(__FILE__), 'data', 'Os.protein.2.fa')
-      left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
-      right = File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
-      cmd = "bundle exec bin/transrate "
-      cmd << " --assembly #{assembly},#{assembly2}"
-      cmd << " --reference #{reference}"
-      cmd << " --left #{left}"
-      cmd << " --right #{right}"
-      c = Transrate::Cmd.new("#{cmd}")
-      c.run
-      assert_equal false, c.status.success?, "exit status"
-    end
-
-  end
-end