class Bio::Velvet::Runner
Public Instance Methods
Detect the binary version currently in use and return as a String
# File lib/bio-velvet/runner.rb, line 85 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 raise VelvetRunnerException, "Error running velveth: #{stderr}\n#{stdout}" end splits = stdout.split("\n") if splits.length > 1 and matches = splits[1].match(/^Version (.+)$/) return matches[1] else 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
# File lib/bio-velvet/runner.rb, line 105 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
Run velveth and then velvetg, with the given kmer size. Returned is a Bio::Velvet::Result
class, stored in a temporary directory. The temporary directory is removed upon program exit.
The velveth_options and velvetg_options are strings to pass as arguments 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 [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]
# File lib/bio-velvet/runner.rb, line 23 def velvet(kmer_length, velveth_options_string, velvetg_options_string='', options={}) res = velveth kmer_length, velveth_options_string, options velvetg res, velvetg_options_string, options end
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).
Further options (the third argument): :velvetg_path: path to the velvetg binary [default: ‘velvetg’]
# File lib/bio-velvet/runner.rb, line 66 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 raise VelvetRunnerException, "Error running velvetg: #{stderr}\n#{stdout}" end velveth_result_object.velvetg_stdout = stdout velveth_result_object.velvetg_stderr = stderr return velveth_result_object end
Run velveth with the given kmer and return a Bio::Velvet::Result
object
Options: :velveth_path: path to the velveth binary [default: ‘velveth’]
# File lib/bio-velvet/runner.rb, line 32 def velveth(kmer_length, velveth_arguments, options={}) set_num_cpus(options[:threads]) result = Result.new outdir = nil if options[:output_assembly_path] log.debug "Using pre-defined assembly directory: #{options[:output_assembly_path] }" outdir = options[:output_assembly_path] else outdir = Files.create.root end result.result_directory = outdir binary = options[:velveth_path] binary ||= 'velveth' # Run velveth 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 raise VelvetRunnerException, "Error running velveth: #{stderr}\n#{stdout}" end result.velveth_stdout = stdout result.velveth_stderr = stderr return result end