sushi_fabric 0.7.2 → 0.7.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 5979375fed31ca635c84b55e996d5fc40254c3de
-  data.tar.gz: 9814016fb3137614502cc9a34fc2e041d6e6e85a
+  metadata.gz: ed4f8e395298758aef808482287e2bf1c5a0bcfe
+  data.tar.gz: d97617cc762c64bf0835cb76a31a6a1dacd51e43
 SHA512:
-  metadata.gz: 42a57301a53a0bd6ea81c66302d38658e4516095853740c279e6abca13c774270f2ab3935e02be1e7aa8f25abfafc62e1f5128953383c18ff7cbf7275637bf89
-  data.tar.gz: 6f152feb2f8466f42c8914591059d406a4873c5030572d6dd4216168f5aa3fa192a8cf907786a3fa9f33cecdb947841fb6450ace952974d64e0e3df9785dc0c0
+  metadata.gz: 6ced57e208f262dd3c0018d5fb2f100961c10fd420a0d23b7330f93a9b6898cd5a2159775b81d313719f92549b0b66e4c22d36aff2a6c7281743d30f28eced28
+  data.tar.gz: d369c6a5bbaebaeff3b7b2522544cec99b5e092e1b9c3f4b6900a398e4be736327d1f90728103e4011f2c05f9b3498af030c003f4f6c8af891785b6549b80091

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20170324-161522'
+# Version = '20170410-034927'
 
 require 'csv'
 require 'fileutils'
@@ -17,6 +17,7 @@ module SushiFabric
     config.gstore_dir = File.join(default_root, 'public/gstore/projects')
     config.sushi_app_dir = default_root
     config.scratch_dir = '/tmp/scratch'
+    config.module_source = nil
   end
 
   # load custmized parameters if there is
@@ -35,6 +36,7 @@ module SushiFabric
     config.gstore_dir = File.join(#{default_root}, 'public/gstore/projects')
     config.sushi_app_dir = #{default_root}
     config.scratch_dir = '/tmp/scratch'
+    config.module_source = nil
   end
 end
       EOF
@@ -46,6 +48,7 @@ end
   GSTORE_DIR = config.gstore_dir
   SUSHI_APP_DIR = config.sushi_app_dir
   SCRATCH_DIR = config.scratch_dir
+  MODULE_SOURCE = config.module_source
   
   unless File.exist?(GSTORE_DIR)
     FileUtils.mkdir_p GSTORE_DIR
@@ -192,6 +195,7 @@ class SushiApp
   attr_reader :analysis_category
   attr_reader :description
   attr_reader :name
+  attr_reader :modules
   attr_accessor :dataset_tsv_file
   attr_accessor :parameterset_tsv_file
   attr_accessor :dataset_sushi_id
@@ -217,6 +221,8 @@ class SushiApp
     @params['process_mode'] = 'SAMPLE'
     @job_ids = []
     @required_columns = []
+    @module_source = MODULE_SOURCE
+    @modules = []
     #@workflow_manager = workflow_manager_instance||DRbObject.new_with_uri(WORKFLOW_MANAGER)
   end
   def set_input_dataset
@@ -360,6 +366,20 @@ class SushiApp
     FileUtils.mkdir_p(@scratch_result_dir)
     FileUtils.mkdir_p(@job_script_dir)
   end
+  def check_latest_module_version(mod)
+    command = "module whatis #{mod}"
+    IO.popen(command) do |io|
+      latest_mod = nil
+      while line = io.gets
+        unless line.chomp.strip.empty?
+          latest_mod = line.split.first
+          break
+        end
+      end
+    end
+    latest_mod = nil if latest_mod == "Failed"
+    latest_mod
+  end
   def job_header
     @scratch_dir = if @params['process_mode'] == 'SAMPLE'
                      @scratch_result_dir + "_" + @dataset['Name'] + '_temp$$'
@@ -372,6 +392,19 @@ class SushiApp
                               else
                                 ''
                               end
+    module_src_command = if @module_source and @modules and !@modules.empty?
+                       "source #{@module_source}"
+                     else
+                       ""
+                     end
+    module_add_commands = if @modules and !@modules.empty?
+                            #modules_with_version = @modules.map{|mod| check_latest_module_version(mod)}
+                            #modules_with_version.compact!
+                            #"module add #{modules_with_version.join(' ')}"
+                            "module add #{@modules.join(' ')}"
+                          else
+                            ""
+                          end
     @out.print <<-EOF
 #!/bin/bash
 #{hold_jid_option}
@@ -386,6 +419,8 @@ echo "Job runs on `hostname`"
 echo "at $SCRATCH_DIR"
 mkdir $SCRATCH_DIR || exit 1
 cd $SCRATCH_DIR || exit 1
+#{module_src_command}
+#{module_add_commands}
 
     EOF
   end

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "0.7.2"
+  VERSION = "0.7.3"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 0.7.2
+  version: 0.7.3
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-03-24 00:00:00.000000000 Z
+date: 2017-04-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler