workflow_manager 0.7.7 → 0.7.8

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 201c8eb50cf7647bf4fa53abbd64586ec05b118a82e0fb053f4102977b3c6cb8
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+  data.tar.gz: ca7beaebea2c29ce6da4dcb15185258aac2f22b57f773017f8f876b36c81643b212d7e09edd528051ee0695138b945fbd13e5201da4e54c4eadada605d15a07b

data/bin/wfm_monitoring

@@ -1,7 +1,7 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
 # 20121112 masa workflow manager client
-Version = '20210625-165025'
+Version = '20211104-160323'
 
 require 'drb/drb' 
 require 'workflow_manager/optparse_ex'
@@ -13,10 +13,11 @@ opt = OptionParser.new do |o|
   o.on(:server, 'druby://localhost:12345', '-d server', '--server', 'workflow manager URI (default: druby://localhost:12345)')
   o.on(:log, '-o logdir', '--logdir', 'directory of standard output and standard error file outputted after the job')
   o.on(:cores, '-c cores', '--cores', 'Number of cores to request for g-sub')
-  o.on(:nodes, '-n nodes', '--nodes', 'Comma separated list of nodes to submit to for g-sub')
+#  o.on(:nodes, '-n nodes', '--nodes', 'Comma separated list of nodes to submit to for g-sub')
   o.on(:ram, '-r RAM', '--RAM', 'Amount of RAM to request in Gigs for g-sub')
   o.on(:scratch, '-s scratch', '--scratch', 'Amount of scratch space to request in Gigs for g-sub')
-  o.on(:queue, '-q queue', '--queue', 'Queue name')
+#  o.on(:queue, '-q queue', '--queue', 'Queue name')
+  o.on(:nice, '-i nice', '--nice', 'Nice')
   o.parse!(ARGV)
 end
 unless script_file = ARGV[0] and script_file =~ /\.sh/
@@ -49,7 +50,8 @@ sge_options = []
 sge_options << "-c #{opt.cores}" if opt.cores
 sge_options << "-r #{opt.ram}" if opt.ram
 sge_options << "-s #{opt.scratch}" if opt.scratch
-sge_options << "-n #{opt.nodes}" if opt.nodes
+#sge_options << "-n #{opt.nodes}" if opt.nodes
+sge_options << "-i #{opt.nice}" if opt.nice
 
 script_content = File.read(script_file)
 workflow_manager = DRbObject.new_with_uri(uri)

data/lib/workflow_manager/cluster.rb

@@ -450,11 +450,15 @@ module WorkflowManager
       partition = if i = options.index("-p")
                     options[i+1]
                   end
+      nice = if i = options.index("-i")
+               options[i+1]
+             end
       new_options = []
       new_options << "--mem=#{ram}G" if ram
       new_options << "-n #{cores}" if cores
       new_options << "--tmp=#{scratch}G" if scratch
       new_options << "-p #{partition}" if partition
+      new_options << "--nice=#{nice}" if nice
       new_options.join(" ")
     end
     def submit_job(script_file, script_content, option='')

data/lib/workflow_manager/version.rb

@@ -1,3 +1,3 @@
 module WorkflowManager
-  VERSION = "0.7.7"
+  VERSION = "0.7.8"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: workflow_manager
 version: !ruby/object:Gem::Version
-  version: 0.7.7
+  version: 0.7.8
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-10-15 00:00:00.000000000 Z
+date: 2021-11-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler