Introduce the <sample_group> place holder.

README.md

@@ -86,10 +86,11 @@ With this mode, PipEngine will submit pipeline jobs to the scheduler.
   -o, --output-dir=<s>          Output directory (override standard output directory names)
   -b, --pbs-opts=<s+>           PBS options
   -q, --pbs-queue=<s>           PBS queue
+  -w, --pbs-set-group=<s>       PBS -W group_list (default: )
   -i, --inspect-pipeline=<s>    Show steps
   --log=<s>                     Log script activities, by default stdin. Options are fluentd (default: stdin)
   -e, --log-adapter=<s>         (stdin|syslog|fluentd) In case of fluentd use http://destination.hostname:port/yourtag
-  --tag=<s+>                    Overwrite tags present in samples.yml and pipeline.yml files (e.g. tag1=value1 tag2=value2)
+
   -h, --help                    Show this message
 ```
 
@@ -651,6 +652,18 @@ within the job script.
 
 If a specific queue needs to be selected for sending the jobs to PBS, the ```--pbs-queue``` (short version **-q**) parameter can be used. This will pass to the ```qsub``` command the ```-q <queue name>``` taken from the command line.
 
+Working in a team can be usefull to share the stdout and stderr of PBS, usually those files (also joined in one single file) have a restricted access just to the owner. To set the group of those files pipengine will automaticcally set the group to the usergroup (primary) by default, otherwise specifying a different group it will be setted accordibly.
+
+```shell
+--pbs-set-group desired_group_name
+```
+
+will become, in the shell script:
+
+```shell
+#PBS -W group_list=desired_group_name
+```
+
 Copyright
 =========
 

VERSION

@@ -1 +1 @@
-0.9.3
+0.9.4

bin/pipengine

@@ -31,6 +31,7 @@ when "run"
 		opt :output_dir, "Output directory (override standard output directory names)", :short => "o", :type => :string
 		opt :pbs_opts, "PBS options", :type => :strings, :short => "b"
 		opt :pbs_queue, "PBS queue", :type => :string, :short => "q"
+		opt :pbs_set_group, "PBS -W group_list", :type => :string, :short => "w", :default => ""
 		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

bio-pipengine.gemspec

@@ -6,7 +6,7 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-pipengine"
-  s.version = "0.9.3"
+  s.version = "0.9.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]

lib/bio-pipengine.rb

@@ -13,3 +13,5 @@
 require 'bio/pipengine/step'
 require 'bio/pipengine/job'
 require 'bio/pipengine'
+
+require 'etc'

lib/bio/pipengine/job.rb

@@ -120,7 +120,15 @@ def to_script(options)
 					file.puts "#!/usr/bin/env bash"
 					file.puts "#PBS -N #{self.name}"
 					file.puts "#PBS -d #{self.output}"
+
 					file.puts "#PBS -q #{options[:pbs_queue]}" if options[:pbs_queue]
+
+					if options[:pbs_set_group].empty?
+						file.puts "#PBS -W group_list=#{Etc.getgrgid(Etc.getpwnam(Etc.getlogin).gid).name}"
+					else
+						file.puts "#PBS -W group_list=#{options[:pbs_set_group]}"
+					end
+
 					if options[:pbs_opts]
 						file.puts "#PBS -l #{options[:pbs_opts].join(",")}"
 					else
@@ -167,14 +175,28 @@ def sub_placeholders(cmd,sample,step=nil)
 				tmp_cmd = cmd.gsub(/<sample>/,sample.name)
 				if tmp_cmd =~/<sample_path>/
 					sample_path_glob = (tmp_cmd.scan(/<sample_path>(\S+)/).map {|e| e.first})
-					if sample_path_glob.empty?
-						tmp_cmd.gsub!(/<sample_path>/,sample.path.join("\s"))
-					else
+					unless sample_path_glob.empty?
 						sample_path_glob.each do |append|
 							tmp_cmd.gsub!(/<sample_path>#{Regexp.quote(append)}/,(sample.path.map {|s| s+append}).join("\s"))
 						end
 					end
+					tmp_cmd.gsub!(/<sample_path>/,sample.path.join("\s"))
 				end
+
+				if tmp_cmd =~/<sample_group>/
+					sample_group_glob = (tmp_cmd.scan(/<sample_group>(\S+)/).map {|e| e.first})
+					unless sample_group_glob.empty?
+						sample_group_glob.each do |append|
+							tmp_cmd.gsub!(/<sample_group>#{Regexp.quote(append)}/,(sample.group+append))
+						end
+					end
+					tmp_cmd.gsub!(/<sample_group>/,sample.group)
+				end
+
+				if tmp_cmd =~/<sample_group\/>/
+					tmp_cmd = tmp_cmd.gsub(/<sample_group\/>/,self.output+"/")
+				end
+
 				# for resourcers and cpus
 				tmp_cmd = sub_resources_and_cpu(tmp_cmd,step)