bio-velvet 0.4.2 → 0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: c74bf34034fed56504e7db21df832117747db1d6
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+  data.tar.gz: 84bcad61582984031f5e34471a84a964c8564485
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+  data.tar.gz: e30e66ded35e8d22a663c942420caa5dd7a87c0adce6c076d18a8b66295b732b439675de976a72b87b6c0582d454d20b0c91f5de0dd2f7176d8c745c2a6e0862

data/Gemfile

@@ -5,6 +5,7 @@ gem 'systemu', '~>2.6'
 gem 'files', '~>0.3'
 gem 'hopcsv', '~> 0.4'
 gem 'bio-commandeer', '~>0.1'
+gem 'parallel', '~>1.3', '>=1.3.3'
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/VERSION

@@ -1 +1 @@
-0.4.2
+0.5.0

data/lib/bio-velvet/graph.rb

@@ -447,7 +447,7 @@ module Bio
             fwd = @ends_of_kmers_of_node[0...10]+'..'
             rev = @ends_of_kmers_of_twin_node[0...10]+'..'
           end
-          "Node #{@node_id}: #{fwd} / #{rev}"
+          "Node from #{@parent_graph.class}: #{@node_id}: #{fwd} / #{rev}"
         end
 
         def inspect

data/lib/bio-velvet/runner.rb

@@ -1,10 +1,12 @@
 require 'files'
 require 'systemu'
+require 'parallel'
 
 module Bio
   module Velvet
     class Runner
       include Bio::Velvet::Logging
+      include Parallel::ProcessorCount
 
       # Run velveth and then velvetg, with the given kmer size. Returned
       # is a Bio::Velvet::Result class, stored in a temporary directory.
@@ -14,13 +16,21 @@ module Bio
       # to velveth and velvetg, respectively.
       #
       # The final options argument is used to specify bio-velvet wrapper options. Currently:
-      # :output_assembly_path: a directory where the assembly takes place (by default, a temporary directory)
+      # :output_assembly_path: a directory where the assembly takes place [default: a temporary directory]
+      # :velveth_path: path to the velveth binary [default: 'velveth']
+      # :velvetg_path: path to the velvetg binary [default: 'velvetg']
+      # :threads: number of threads to use [default: all threads on the machine]
       def velvet(kmer_length, velveth_options_string, velvetg_options_string='', options={})
         res = velveth kmer_length, velveth_options_string, options
-        velvetg res, velvetg_options_string
+        velvetg res, velvetg_options_string, options
       end
 
+      # Run velveth with the given kmer and return a Bio::Velvet::Result object
+      #
+      # Options:
+      # :velveth_path: path to the velveth binary [default: 'velveth']
       def velveth(kmer_length, velveth_arguments, options={})
+        set_num_cpus(options[:threads])
         result = Result.new
         outdir = nil
         if options[:output_assembly_path]
@@ -31,8 +41,11 @@ module Bio
         end
         result.result_directory = outdir
 
+        binary = options[:velveth_path]
+        binary ||= 'velveth'
+
         # Run velveth
-        cmd = "velveth #{result.result_directory} #{kmer_length} #{velveth_arguments}"
+        cmd = "#{binary} #{result.result_directory} #{kmer_length} #{velveth_arguments}"
         log.info "Running velveth: #{cmd}" if log.info?
         status, stdout, stderr = systemu cmd
         if status.exitstatus != 0
@@ -47,8 +60,15 @@ module Bio
       # Run velvetg, with a Bio::Velvet::Result object
       # generated with velveth, and velvetg arguments as a String (no need to specify the velvet directory, just the extra
       # arguments).
-      def velvetg(velveth_result_object, velvetg_arguments)
-        cmd = "velvetg #{velveth_result_object.result_directory} #{velvetg_arguments}"
+      #
+      # Further options (the third argument):
+      # :velvetg_path: path to the velvetg binary [default: 'velvetg']
+      def velvetg(velveth_result_object, velvetg_arguments, options={})
+        binary = options[:velvetg_path]
+        binary ||= 'velvetg'
+
+        cmd = "#{binary} #{velveth_result_object.result_directory} #{velvetg_arguments}"
+
         log.info "Running velvetg: #{cmd}" if log.info?
         status, stdout, stderr = systemu cmd
         if status.exitstatus != 0
@@ -62,8 +82,8 @@ module Bio
 
       # Detect the binary version currently in use and return
       # as a String
-      def binary_version
-        cmd = 'velveth'
+      def binary_version(velveth_path='velveth')
+        cmd = velveth_path
         log.info "Running velveth: #{cmd}" if log.info?
         status, stdout, stderr = systemu cmd
         if status.exitstatus != 0
@@ -76,6 +96,18 @@ module Bio
           raise "Unable to parse the version number from running `#{cmd}', the output was: #{stdout}"
         end
       end
+
+      # According to the manual,
+      #"Velvet will the use up to OMP_NUM_THREADS+1 or OMP_THREAD_LIMIT threads."
+      #
+      # Argument is the number of CPUs, or nil if all CPUs on the machine are
+      # to be used
+      def set_num_cpus(num_cpus=nil)
+        num_cpus ||= processor_count #from the parallel gem
+        log.debug "Setting number of CPUs to run velvet with to #{num_cpus}."
+        ENV['OMP_NUM_THREADS'] = (num_cpus - 1).to_s
+        ENV['OMP_THREAD_LIMIT'] = num_cpus.to_s
+      end
     end
 
     class VelvetRunnerException < Exception; end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-velvet
 version: !ruby/object:Gem::Version
-  version: 0.4.2
+  version: 0.5.0
 platform: ruby
 authors:
 - Ben J Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-15 00:00:00.000000000 Z
+date: 2015-01-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger
@@ -80,6 +80,26 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: parallel
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.3.3
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.3.3
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement