bio-grid 0.3.1 → 0.3.2

data/VERSION

@@ -1 +1 @@
-0.3.1
+0.3.2

data/bin/bio-grid

@@ -56,6 +56,10 @@ optparse = OptionParser.new do |opts|
 		options[:sep] = sep
 	end
 
+	opts.on("--uuid UUID","Provide a UUID for the job array") do |uuid|
+		options[:uuid] = uuid
+	end
+
 	opts.on("--keep-scripts","Keep all the running scripts created for all the jobs") {options[:keep] = true}
 
 	opts.on("-h","--help","Display this screen") do

data/bio-grid.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-grid"
-  s.version = "0.3.1"
+  s.version = "0.3.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Francesco Strozzi"]
-  s.date = "2012-09-25"
+  s.date = "2012-10-12"
   s.description = "A BioGem to submit jobs on a queue system"
   s.email = "francesco.strozzi@gmail.com"
   s.executables = ["bio-grid"]
@@ -37,7 +37,7 @@ Gem::Specification.new do |s|
   s.homepage = "http://github.com/fstrozzi/bioruby-grid"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.24"
+  s.rubygems_version = "1.8.23"
   s.summary = "A BioGem to submit jobs on a queue system"
 
   if s.respond_to? :specification_version then

data/lib/bio/grid.rb

@@ -3,16 +3,16 @@ module Bio
 	class Grid
 	
 		attr_accessor :input,:number,:uuid
-		def initialize(input,number)
+		def initialize(input,number, uuid)
 			@input = input
 			@number = number
-			@uuid = UUID.new.generate.split("-").first
+			@uuid = uuid ? uuid : UUID.new.generate.split("-").first 
 		end
 
 		def self.run(options)
 			options[:number] = "all" unless options[:number]
-			grid = self.new options[:input], options[:number]
-			options[:uuid] = grid.uuid
+			grid = self.new options[:input], options[:number], options[:uuid]
+			options[:uuid] = grid.uuid unless options[:uuid]
 			groups = grid.prepare_input_groups
 			inputs = groups.keys.sort
 			groups[inputs.shift].each_with_index do |input1,index|

data/lib/bio/grid/job.rb

@@ -22,7 +22,7 @@ module Bio
 				if commandline =~/<output>\.(\S+)/
 					extension = $1
 					commandline.gsub!(/<output>/,job_output)	
-					job_output << ".#{extension}"
+					#job_output << ".#{extension}"
 				else
 					self.options[:output_folder] = true
 					commandline.gsub!(/<output>/,job_output)
@@ -35,12 +35,12 @@ module Bio
 				if self.options[:copy]
 					self.instructions << ("mkdir -p #{self.options[:copy]}\n")
 					copy_type = (self.options[:output_folder]) ? "cp -r" : "cp"
-					self.instructions << ("#{copy_type} #{self.job_output} #{self.options[:copy]}\n")
+					self.instructions << ("#{copy_type} #{self.job_output}* #{self.options[:copy]}\n")
 				end
 
 				if self.options[:clean]
 					rm_type = (self.options[:output_folder]) ? "rm -fr" : "rm -f"
-					self.instructions << ("#{rm_type} #{self.job_output}\n")
+					self.instructions << ("#{rm_type} #{self.job_output}*\n")
 				end	
 			end
 
@@ -62,11 +62,11 @@ module Bio
 
 			def	execute(command_line,inputs,input1,groups,index)
 				self.set_scheduler_options(:pbs) # set script specific options for the scheduling system
-        self.set_commandline(command_line,inputs,input1,groups,index)
+        		self.set_commandline(command_line,inputs,input1,groups,index)
 				self.set_output_dir
-        self.append_options
-        job_filename = (self.options[:keep]) ? "job_#{index+1}#{self.options[:parameter_value]}.sh" : "job.sh"
-        self.run(job_filename)
+        		self.append_options
+        		job_filename = (self.options[:keep]) ? "job_#{index+1}#{self.options[:parameter_value]}.sh" : "job.sh"
+        		self.run(job_filename)
 			end
 
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-grid
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.3.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-09-25 00:00:00.000000000 Z
+date: 2012-10-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: uuid
@@ -146,7 +146,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -4026493835135905673
+      hash: -3879853977881312685
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -155,7 +155,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: A BioGem to submit jobs on a queue system