bio-pipengine 0.8.2 → 0.9.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: bc9d13da2c214f7cb703c5f7122c1ace4285230a
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+  data.tar.gz: 4fbe9029f9164019773464d76dce673a9a295cc6
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data/VERSION

@@ -1 +1 @@
-0.8.2
+0.9.0

data/bin/pipengine

@@ -34,6 +34,7 @@ when "run"
 		opt :inspect_pipeline, "Show steps", :short => "i", :type => :string
 		opt :log, "Log script activities, by default stdin. Options are fluentd", :type => :string, :default => "stdin"
 		opt :log_adapter, "(stdin|syslog|fluentd) In case of fluentd use http://destination.hostname:port/yourtag", :type => :string
+		opt :tag, "Overwrite tags present in samples.yml and pipeline.yml files (e.g. tag1=value1 tag2=value2)", :type => :strings
 	end
 #when "jobs"
 #	ARGV.shift

data/lib/bio/pipengine.rb

@@ -50,6 +50,24 @@ module Bio
 			end
 		end
 
+		def self.parse_tag_option(option_tag)
+			if !option_tag
+				return {}	
+			else
+				tags = {}
+				option_tag.each do |tag|
+					values = tag.split("=")
+					if values.empty?
+						@@logger_error.error "\nAbort! Unrecognized values for tag option, please provide the tags as follows: tag1=value1 tag2=value2".red
+						exit
+					else
+						tags.merge! Hash[*values.flatten]
+					end
+				end
+				return tags
+			end	
+		end
+
 		# handle steps that run on multiple samples (i.e. sample groups job)
 		def self.check_and_run_multi(samples_file,pipeline,samples_list,options)
 			step_multi = options[:steps].map {|s| Bio::Pipengine::Step.new(s,pipeline["steps"][s]).is_multi?}
@@ -86,8 +104,11 @@ module Bio
 			job.local = options[:tmp]
 			job.custom_output = options[:output_dir]
 			job.custom_name = (options[:name]) ? options[:name] : nil
+			# Adding pipeline and samples resources
 			job.add_resources pipeline["resources"]
 			job.add_resources samples_file["resources"]
+			# Adding resource tag from the command line which can overwrite resources defined in the pipeline and samples files
+			job.add_resources parse_tag_option(options[:tag])
 			#setting the logging system
 			job.log = options[:log]
 			job.log_adapter = options[:log_adapter]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-pipengine
 version: !ruby/object:Gem::Version
-  version: 0.8.2
+  version: 0.9.0
 platform: ruby
 authors:
 - Francesco Strozzi
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-11 00:00:00.000000000 Z
+date: 2016-04-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: trollop