transfuse 0.4.6 → 0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  metadata.gz: 8875ba5243bd12d1f74f35879f2c505ffd480881
-  data.tar.gz: 98c7665892f464bb62eeeb6901d3e7305491699f
+  metadata.gz: 1d2ce7c587a22651d2541e9364d89e2f49ed67eb
+  data.tar.gz: 9b427e13469f85666a8b0f762ec41335e840d090
 SHA512:
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-  data.tar.gz: 39cab59f74296f2be2893906cc19d33212fab43f7e3643a4b1bead5ce3bdafa8b49a62623f625e67b61583f48f767c1675791cd3cf2fc5614e9fa0004cab3dae
+  metadata.gz: faaca3cb15a3268be4d0ac816d71721c58910c8215175aa9bd170b893898aacc34ce5bae146acf2514ee0042b4354ec83cf6fe3b6c2d2cb403b28a8dfae4340f
+  data.tar.gz: bc5ec2f21f650869f112ab7afa10e2bd55066414505afccc2a182ada3737a0e98622738e3dee73d695f0b0e97561ec3fb4e106893c8b9546e3067cb982eebaa7

data/.gitignore

@@ -1,3 +1,36 @@
+
+*.gem
+*.rbc
+*.so
+.bundle
+.config
+coverage
+test_data
+InstalledFiles
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+*~
+.#*
+\#*
+*so
+
 # directories
 
-coverage
+coverage
+
+# vagrant stuff
+.vagrant
+
+# packaging stuff
+*.tar.gz
+packaging/bindeps
+packaging/vendor
+packaging/packaging
+traveling-ruby*
+*box
+

data/README.md

@@ -2,25 +2,11 @@
 
 Transfuse intelligently merges your multiple de novo transcriptome assemblies. Run multiple assemblies with different de novo assemblers, or different settings in the same assembler and have them combined into a single high quality transcriptome.
 
-Transfuse takes in the reads you used to do the assembly and a list of fasta files and produces a single output fasta file.
+Transfuse takes in the reads you used to perform your transcriptome assembly and a list of your assemblies as fasta files and produces a single output fasta file.
 
 ### Installation and Running
 
-To install Transfuse you can get it from rubygems.com
-
-`gem install transfuse`
-
-or you can clone this repo:
-
-`git clone https://github.com/cboursnell/transfuse.git`
-
-then build and install the ruby gem
-
-`gem build *spec; gem install *gem`
-
-Transfuse also requires `vsearch` to be installed which can be downloaded from:
-
-`https://github.com/torognes/vsearch`
+Download the latest release and unpack it. This package contains everything that transfuse needs including a version of ruby. 
 
 ### Usage
 
@@ -40,7 +26,9 @@ Transfuse is run on the command line. The options are:
 
 An example command:
 
-`transfuse --assembly soap-k31.fa,soap-k41.fa,soap-k51.fa --left reads_1.fq --right reads_2.fq --output soap-merged.fa --threads 12`
+```
+transfuse --assemblies soap-k31.fa,soap-k41.fa,soap-k51.fa --left reads_1.fq --right reads_2.fq --output soap-merged.fa --threads 12
+```
 
 ### Contributing
 

data/Rakefile

@@ -24,3 +24,100 @@ end
 
 desc "Run tests"
 task :default => :test
+
+# packaging
+
+require 'bundler/setup'
+
+PACKAGE_NAME = "transfuse"
+VERSION = "0.5.0"
+TRAVELING_RUBY_VERSION = "20150210-2.2.0"
+
+desc "Package your app"
+task :package => ['package:linux', 'package:osx']
+
+namespace :package do
+
+  desc "Package your app for Linux x86_64"
+  task :linux => [:bundle_install, "packaging/packaging/traveling-ruby-#{TRAVELING_RUBY_VERSION}-linux-x86_64.tar.gz"] do
+    create_package("linux-x86_64")
+  end
+
+  desc "Package your app for OS X"
+  task :osx => [:bundle_install, "packaging/packaging/traveling-ruby-#{TRAVELING_RUBY_VERSION}-osx.tar.gz"] do
+    create_package("osx")
+  end
+
+  file "packaging/packaging/traveling-ruby-#{TRAVELING_RUBY_VERSION}-linux-x86_64.tar.gz" do
+    download_runtime("linux-x86_64")
+  end
+
+  file "packaging/packaging/traveling-ruby-#{TRAVELING_RUBY_VERSION}-osx.tar.gz" do
+    download_runtime("osx")
+  end
+
+  desc "Install gems to local directory"
+  task :bundle_install do
+    if RUBY_VERSION !~ /^2\.2\./
+      abort "You can only 'bundle install' using Ruby 2.2, because that's what Traveling Ruby uses."
+    end
+    Bundler.with_clean_env do
+      sh "env BUNDLE_IGNORE_CONFIG=1 bundle install --path packaging/vendor"
+    end
+    sh "rm -f packaging/vendor/*/*/cache/*"
+  end
+end
+
+def create_package(target)
+  package_pref = "#{PACKAGE_NAME}-#{VERSION}-#{target}"
+  package_dir = File.join("packaging", package_pref)
+  sh "rm -rf #{package_dir}"
+  sh "mkdir -p #{package_dir}/lib/app"
+
+  # copy things from gem to package
+  sh "cp -r bin #{package_dir}/lib/" # bin
+  sh "cp -r lib #{package_dir}/lib/" # lib
+  sh "cp -r deps #{package_dir}/lib/" # deps
+  sh "cp files.txt #{package_dir}/lib/" # deps
+  sh "cp Gemfile* #{package_dir}/lib/" # Gemfiles
+  sh "cp *gemspec #{package_dir}/lib/" # gemspec
+
+  # download travelling ruby
+  sh "mkdir #{package_dir}/lib/ruby"
+  sh "tar -xzf packaging/packaging/traveling-ruby-#{TRAVELING_RUBY_VERSION}-#{target}.tar.gz -C #{package_dir}/lib/ruby"
+  sh "cp packaging/transfuse #{package_dir}/transfuse"
+  sh "cp -pR packaging/vendor/* #{package_dir}/lib/"
+  sh "cp Gemfile Gemfile.lock #{package_dir}/lib/"
+
+  # install binary dependencies
+  sh "mkdir -p #{package_dir}/bin"
+  sh "mkdir -p #{package_dir}/lib"
+  sh "wget -nc https://github.com/Blahah/snap/releases/download/v1.0beta.18/snap_v1.0beta.18_linux.tar.gz"
+  sh "wget -nc https://github.com/Blahah/transrate-tools/releases/download/v1.0.0/bam-read_v1.0.0_linux.tar.gz"
+  sh "wget -nc https://github.com/COMBINE-lab/salmon/releases/download/v0.4.2/SalmonBeta-0.4.2_DebianSqueeze.tar.gz"
+  sh "wget -nc https://github.com/torognes/vsearch/releases/download/v1.9.5/vsearch-1.9.5-linux-x86_64.tar.gz"
+  sh "find . -maxdepth 1 -name '*.tar.gz' -exec tar xzf '{}' \\;" # unpack
+  sh "cp snap-aligner #{package_dir}/bin/."
+  sh "cp bam-read #{package_dir}/bin/."
+  sh "cp SalmonBeta-0.4.2_DebianSqueeze/bin/salmon #{package_dir}/bin/."
+  sh "cp -r SalmonBeta-0.4.2_DebianSqueeze/lib/* #{package_dir}/lib/."
+  sh "cp vsearch-1.9.5-linux-x86_64/bin/vsearch #{package_dir}/bin/."
+
+  sh "cp packaging/libruby.* #{package_dir}/lib/."
+
+  sh "mkdir #{package_dir}/lib/.bundle"
+  sh "cp packaging/bundler-config #{package_dir}/lib/.bundle/config"
+  # create package
+  if !ENV['DIR_ONLY']
+    sh "cd packaging && tar -czf #{package_pref}.tar.gz #{package_pref}"
+    sh "rm -rf #{package_dir}"
+  end
+  sh "rm -rf packaging/vendor packaging/bindeps .bundle"
+
+end
+
+def download_runtime(target)
+  sh "mkdir -p packaging/packaging &&" +
+     "cd packaging/packaging && curl -L -O --fail " +
+     "http://d6r77u77i8pq3.cloudfront.net/releases/traveling-ruby-#{TRAVELING_RUBY_VERSION}-#{target}.tar.gz"
+end

data/bin/transfuse

@@ -31,22 +31,22 @@ opts = Trollop::options do
   opt :output, "write merged assembly to file", :type => String
   opt :threads, "number of threads", :type => :int, :default => 1
   opt :id, "sequence identity to cluster at", :type => :float, :default => 1.0
-  # opt :install, "install dependencies"
+  opt :install, "install dependencies"
   opt :verbose, "be verbose"
 end
 
 transfuse = Transfuse::Transfuse.new opts.threads, opts.verbose
 
-# if opts.install
-#   transfuse.install_dependencies
-# else
-#   missing = transfuse.check_dependencies
-#   unless missing.empty?
-#     list = missing.collect {|i| "#{i.name}:#{i.version}"}.join("\n - ")
-#     msg = "Not installed: \n - #{list}"
-#     abort msg
-#   end
-# end
+if opts.install
+  transfuse.install_dependencies
+  abort "Everything installed"
+end
+missing = transfuse.check_dependencies
+unless missing.empty?
+  list = missing.collect {|i| "#{i.name}:#{i.version}"}.join("\n - ")
+  msg = "Not installed: \n - #{list}"
+  abort msg
+end
 
 assembly_files = transfuse.check_files(opts.assemblies, "assemblies")
 left = transfuse.check_files(opts.left, "left")

data/deps/deps.yaml

@@ -2,10 +2,59 @@ vsearch:
   binaries:
     - vsearch
   version:
-    number: '1.1.3'
+    number: '1.8.0'
     command: 'vsearch --version'
   url:
     64bit:
-      linux: https://github.com/torognes/vsearch/releases/download/v1.1.3/vsearch-1.1.3-linux-x86_64
-      macosx: https://github.com/torognes/vsearch/releases/download/v1.1.3/vsearch-1.1.3-osx-x86_64
-  unpack: false
+      linux: https://github.com/torognes/vsearch/releases/download/v1.8.0/vsearch-1.8.0-linux-x86_64.tar.gz
+      macosx: https://github.com/torognes/vsearch/releases/download/v1.8.0/vsearch-1.8.0-osx-x86_64.tar.gz
+  unpack: true
+snap:
+  binaries:
+    - snap-aligner
+  version:
+    number: '1.0beta.18'
+    command: 'snap-aligner'
+  url:
+    64bit:
+      linux: https://github.com/Blahah/snap/releases/download/v1.0beta.18/snap_v1.0beta.18_linux.tar.gz
+      macosx: https://github.com/Blahah/snap/releases/download/v1.0beta.18/snap_v1.0beta.18_osx.tar.gz
+bam-read:
+  binaries:
+   - bam-read
+  version:
+    number: '1.0.0'
+    command: 'bam-read'
+  url:
+    64bit:
+      linux: https://github.com/Blahah/transrate-tools/releases/download/v1.0.0/bam-read_v1.0.0_linux.tar.gz
+      macosx: https://github.com/Blahah/transrate-tools/releases/download/v1.0.0/bam-read_v1.0.0_osx.tar.gz
+  unpack: true
+salmon:
+  binaries:
+    - salmon
+  libraries:
+    - libgcc_s.so.1
+    - libgomp.so.1
+    - libm.so.6
+    - librt.so.1
+    - libstdc++.so.6
+    - libtbb.so
+    - libtbb.so.2
+    - libtbbmalloc.so
+    - libtbbmalloc.so.2
+    - libtbbmalloc_proxy.so
+    - libtbbmalloc_proxy.so.2
+    - libcmph.0.dylib
+    - libcmph.dylib
+    - libtbb.dylib
+    - libtbbmalloc.dylib
+    - libtbbmalloc_proxy.dylib
+    - libsalmon_core.a
+  version:
+    number: '0.4'
+    command: 'salmon -v'
+  url:
+    64bit:
+      linux: https://github.com/COMBINE-lab/salmon/releases/download/v0.4.2/SalmonBeta-0.4.2_DebianSqueeze.tar.gz
+      macosx: https://github.com/COMBINE-lab/salmon/releases/download/v0.4.2/SalmonBeta-0.4.2_OSX-10.10.tar.gz

data/files.txt

@@ -0,0 +1,28 @@
+.gitignore
+Gemfile
+README.md
+Rakefile
+bin/transfuse
+deps/deps.yaml
+files.txt
+lib/transfuse.rb
+lib/transfuse/cluster.rb
+lib/transfuse/cmd.rb
+lib/transfuse/consensus.rb
+lib/transfuse/transfuse.rb
+lib/transfuse/version.rb
+notes.md
+packaging/build_deps_linux.sh
+packaging/build_deps_macosx.sh
+packaging/bundler-config
+packaging/minify.sh
+packaging/transfuse
+test/data/assembly1.fasta
+test/data/assembly2.fasta
+test/data/contig_scores1.csv
+test/helper.rb
+test/test_cluster.rb
+test/test_transfuse.rb
+test/vagrant/linux-x86_64/Vagrantfile
+test/vagrant/linux-x86_64/provision.sh
+transfuse.gemspec

data/lib/transfuse/consensus.rb

@@ -86,7 +86,6 @@ module Transfuse
               out.write "#{s[1]}\n"
             end
 
-
           end # msa.each
         end # file
       end # file open

data/lib/transfuse/transfuse.rb

@@ -191,10 +191,20 @@ module Transfuse
     end
 
     def transrate files, left, right
+      unless left.is_a?(Array)
+        left = [left]
+      end
+      unless right.is_a?(Array)
+        right = [right]
+      end
       scores = {}
       shortname = ""
       files.each do |n|
-        shortname << File.basename(n, File.extname(n))[0..4]
+        a = File.basename(n).split("_").first
+        if a.length > 5
+          a = a[0..4]
+        end
+        # shortname << File.basename(n, File.extname(n))[0..4]
       end
       scores_file = "#{shortname}_scores.csv"
       if File.exist?(scores_file)

data/lib/transfuse/version.rb

@@ -7,8 +7,8 @@ module Transfuse
   # Semantic Versioning 2.0 (http://semver.org/).
   module VERSION
     MAJOR = 0
-    MINOR = 4
-    PATCH = 6
+    MINOR = 5
+    PATCH = 0
     BUILD = nil
 
     STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')

data/packaging/build_deps_linux.sh

@@ -0,0 +1,17 @@
+echo "don't use this"
+
+export PATH=~/gcc-4.8.4/bin:~/cmake-3.1.3-Linux-x86_64/bin:$PATH
+
+cd ~
+
+# vsearch
+wget https://github.com/torognes/vsearch/releases/download/v1.8.0/vsearch-1.8.0-linux-x86_64.tar.gz
+tar xzf vsearch-1.8.0-linux-x86_64.tar.gz
+cd vsearch-1.8.0-linux-x86_64
+cd bin
+tar zcvf vsearch.tar.gz vsearch
+## package it up
+cp vsearch.tar.gz /vagrant/
+
+
+

data/packaging/build_deps_macosx.sh

@@ -0,0 +1 @@
+echo "mac osx not supported yet"

data/packaging/bundler-config

@@ -0,0 +1,2 @@
+BUNDLE_PATH: .
+BUNDLE_DISABLE_SHARED_GEMS: '1'

data/packaging/minify.sh

@@ -0,0 +1,43 @@
+#! /bin/sh
+
+# Remove tests
+rm -rf lib/app/ruby/*/gems/*/test
+rm -rf lib/app/ruby/*/gems/*/tests
+rm -rf lib/app/ruby/*/gems/*/spec
+rm -rf lib/app/ruby/*/gems/*/features
+rm -rf lib/app/ruby/*/gems/*/benchmark
+
+# Remove documentation
+rm -f lib/app/ruby/*/gems/*/README*
+rm -f lib/app/ruby/*/gems/*/CHANGE*
+rm -f lib/app/ruby/*/gems/*/Change*
+rm -f lib/app/ruby/*/gems/*/COPYING*
+rm -f lib/app/ruby/*/gems/*/LICENSE*
+rm -f lib/app/ruby/*/gems/*/MIT-LICENSE*
+rm -f lib/app/ruby/*/gems/*/*.txt
+rm -f lib/app/ruby/*/gems/*/*.md
+rm -f lib/app/ruby/*/gems/*/*.rdoc
+rm -rf lib/app/ruby/*/gems/*/doc
+rm -rf lib/app/ruby/*/gems/*/docs
+rm -rf lib/app/ruby/*/gems/*/example
+rm -rf lib/app/ruby/*/gems/*/examples
+rm -rf lib/app/ruby/*/gems/*/sample
+rm -rf lib/app/ruby/*/gems/*/doc-api
+find lib/app/ruby -name '*.md' | xargs rm -f
+
+# Remove misc unnecessary files
+rm -rf lib/app/ruby/*/gems/*/.gitignore
+rm -rf lib/app/ruby/*/gems/*/.travis.yml
+
+# Remove leftover native extension sources
+rm -f lib/app/ruby/*/gems/*/ext/Makefile
+rm -f lib/app/ruby/*/gems/*/ext/*/Makefile
+find lib/app/ruby -name '*.c' | xargs rm -f
+find lib/app/ruby -name '*.cpp' | xargs rm -f
+find lib/app/ruby -name '*.h' | xargs rm -f
+find lib/app/ruby -name '*.rl' | xargs rm -f
+find lib/app/ruby -name 'extconf.rb' | xargs rm -f
+
+# Remove Java files. They're only used for JRuby support
+find lib/app/ruby -name '*.java' | xargs rm -f
+find lib/app/ruby -name '*.class' | xargs rm -f

data/packaging/transfuse

@@ -0,0 +1,20 @@
+#!/bin/bash
+set -e
+
+# Figure out where this script is located.
+SELFDIR="`dirname \"$0\"`"
+SELFDIR="`cd \"$SELFDIR\" && pwd`"
+
+# Temporarily set PATH and LD_LIBRARY_PATH
+export PATH=$SELFDIR/bin:$PATH
+export LD_LIBRARY_PATH=$SELFDIR/lib:$LD_LIBRARY_PATH
+export DYLD_FALLBACK_LIBRARY_PATH=$SELFDIR/lib:$DYLD_FALLBACK_LIBRARY_PATH
+# Tell Bundler where the Gemfile and gems are.
+export BUNDLE_GEMFILE="$SELFDIR/lib/Gemfile"
+unset BUNDLE_IGNORE_CONFIG
+
+# Tell transfuse this is the packaged version
+# export TRANSFUSE_PACKAGED_BINARY=true
+
+# Run the actual app using the bundled Ruby interpreter, with Bundler activated.
+exec "$SELFDIR/lib/ruby/bin/ruby" -rbundler/setup "$SELFDIR/lib/bin/transfuse" $@

data/test/vagrant/linux-x86_64/Vagrantfile

@@ -0,0 +1,12 @@
+# -*- 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
+                                                                
+  config.vm.provision "shell", path: "provision.sh"
+end

data/test/vagrant/linux-x86_64/provision.sh

@@ -0,0 +1,35 @@
+su vagrant
+
+# Setup
+sudo apt-get update -y
+sudo apt-get install -y curl build-essential git zlib1g zlib1g-dev cmake emacs23-nox
+
+# Install a multi-user RVM install with the latest ruby
+wget https://keybase.io/mpapis/key.asc
+gpg --import key.asc
+
+\curl -sSL https://get.rvm.io | bash -s stable --ruby
+
+source /home/vagrant/.rvm/scripts/rvm
+
+# Add user to RVM group
+#sudo usermod -a -G rvm vagrant
+
+# Install dependencies
+gem install bundler rake
+
+# Install transrate
+#git clone https://github.com/Blahah/transrate.git
+#cd transrate
+#gem build *spec
+#gem install *gem
+#rm *gem
+#cd ..
+
+# Install transfuse
+git clone https://github.com/cboursnell/transfuse.git
+cd transfuse
+sudo chmod -R 775 .
+
+
+#bundle exec rake package:linux

data/transfuse.gemspec

@@ -4,12 +4,12 @@ require File.expand_path('../lib/transfuse/version', __FILE__)
 Gem::Specification.new do |gem|
   gem.name        = 'transfuse'
   gem.version     = Transfuse::VERSION::STRING.dup
-  gem.date        = '2015-05-22'
+  gem.date        = '2015-12-01'
   gem.summary     = "Merge multiple transcriptome assemblies"
   gem.description = "See summary"
-  gem.authors     = ["Richard Smith-Unna", "Chris Boursnell"]
-  gem.email       = ['rds45@cam.ac.uk', 'cmb211@cam.ac.uk']
-  gem.files       = `git ls-files`.split("\n")
+  gem.authors     = ["Chris Boursnell", "Richard Smith-Unna"]
+  gem.email       = ['cmb211@cam.ac.uk', 'rds45@cam.ac.uk']
+  gem.files       = File.readlines('files.txt').map { |f| f.chomp }
   gem.executables = ["transfuse"]
   gem.require_paths = %w( lib )
   gem.homepage    = 'https://github.com/cboursnell/transfuse'

metadata

@@ -1,15 +1,15 @@
 --- !ruby/object:Gem::Specification
 name: transfuse
 version: !ruby/object:Gem::Version
-  version: 0.4.6
+  version: 0.5.0
 platform: ruby
 authors:
-- Richard Smith-Unna
 - Chris Boursnell
+- Richard Smith-Unna
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-05-22 00:00:00.000000000 Z
+date: 2015-12-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: transrate
@@ -213,8 +213,8 @@ dependencies:
         version: 0.8.2
 description: See summary
 email:
-- rds45@cam.ac.uk
 - cmb211@cam.ac.uk
+- rds45@cam.ac.uk
 executables:
 - transfuse
 extensions: []
@@ -226,6 +226,7 @@ files:
 - Rakefile
 - bin/transfuse
 - deps/deps.yaml
+- files.txt
 - lib/transfuse.rb
 - lib/transfuse/cluster.rb
 - lib/transfuse/cmd.rb
@@ -233,12 +234,19 @@ files:
 - lib/transfuse/transfuse.rb
 - lib/transfuse/version.rb
 - notes.md
+- packaging/build_deps_linux.sh
+- packaging/build_deps_macosx.sh
+- packaging/bundler-config
+- packaging/minify.sh
+- packaging/transfuse
 - test/data/assembly1.fasta
 - test/data/assembly2.fasta
 - test/data/contig_scores1.csv
 - test/helper.rb
 - test/test_cluster.rb
 - test/test_transfuse.rb
+- test/vagrant/linux-x86_64/Vagrantfile
+- test/vagrant/linux-x86_64/provision.sh
 - transfuse.gemspec
 homepage: https://github.com/cboursnell/transfuse
 licenses: