sushi_fabric 1.0.1 → 1.0.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 6bb6ed61655c7decac6439f7bd3c73784888ae9686d2611c10f9d4c40bda0621
-  data.tar.gz: 91e98688ac53cfc55560decb2537ee1b38e9c93d24ffb4cfae02875088e2e910
+  metadata.gz: cfe59c9648980949d93b531a0bd3346d46b7dc21c9feea0a81deb7a30c13fc9e
+  data.tar.gz: f29b974e1bbc6d6d47895ec6ff8a4789623542ff176ab53455b23308a838db2d
 SHA512:
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-  data.tar.gz: b5ee9600a1e1b2fe1d76b27bc37cc30a230a5cafb0e613fb5ab13f587ddade33e8f365c87be81e315239d78fb90c99bffe9f65d5ede95f62c8947c1c540be75a
+  metadata.gz: 7325be618b4e21089db068e04b99fa48d2e40452ee9e3646aec7600ba59e7a30de6d0e56faacd1bd75a13d442677c5c735dfda367041e03e5e71804a5fcc4a4a
+  data.tar.gz: ce5e49baed8af919d9803b3dfbfbcb7e6c47c789c4b06224db46e53fbf4c7277cf7cf412dafe212ec6688399651a160af07d9e62a196f092b005fda7b39d482a

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20201105-115625'
+# Version = '20210205-155336'
 
 require 'csv'
 require 'fileutils'
@@ -228,6 +228,8 @@ class SushiApp
   attr_accessor :input_dataset_bfabric_application_number
   attr_accessor :next_dataset_bfabric_application_number
   attr_reader :inactivate_nodes
+  attr_reader :employee
+
   def initialize
     @gstore_dir = GSTORE_DIR
     @project = nil
@@ -238,6 +240,7 @@ class SushiApp
     @params['scratch'] = nil
     @params['node'] = ''
     @params['queue'] = ''
+    @params['partition'] = ''
     @params['process_mode'] = 'SAMPLE'
     @params['samples'] = ''
     @job_ids = []
@@ -391,7 +394,7 @@ class SushiApp
     FileUtils.mkdir_p(@job_script_dir)
   end
   def check_latest_modules_version(modules)
-    command_out =  %x[ bash -lc "source #{@module_source}; module whatis #{modules.join(" ")} 2>&1" | cut -f 1 -d " " | sort | uniq ]
+    command_out =  %x[ bash -lc "source #{@module_source}; module whatis #{modules.join(" ")} 2>&1" | cut -f 1 -d " " | uniq ]
     latest_modules = []
     command_out.split("\n").each do |line_|
       line = line_.chomp
@@ -410,8 +413,8 @@ class SushiApp
                      @scratch_result_dir + '_temp$$'
                    end
     hold_jid_option = if @dataset_sushi_id and parent_data_set = DataSet.find_by_id(@dataset_sushi_id.to_i) and !parent_data_set.jobs.empty?
-                                parent_data_set_job_ids = parent_data_set.jobs.map{|job| job.submit_job_id}.join(",")
-                                "#\$ -hold_jid #{parent_data_set_job_ids}"
+                                parent_data_set_job_ids = parent_data_set.jobs.map{|job| job.submit_job_id}.join(":")
+                                "#SBATCH --dependency=afterany:#{parent_data_set_job_ids}"
                               else
                                 ''
                               end
@@ -494,6 +497,7 @@ rm -rf #{@scratch_dir} || exit 1
     gsub_options = []
     gsub_options << "-c #{@params['cores']}" unless @params['cores'].to_s.empty?
     gsub_options << "-n #{@params['node']}" unless @params['node'].to_s.empty?
+    gsub_options << "-p #{@params['partition']}" unless @params['partition'].to_s.empty?
     gsub_options << "-r #{@params['ram']}" unless @params['ram'].to_s.empty?
     gsub_options << "-s #{@params['scratch']}" unless @params['scratch'].to_s.empty?
     command = "wfm_monitoring --server #{WORKFLOW_MANAGER} --user #{@user} --project #{@project.gsub(/p/,'')} --logdir #{@gstore_script_dir} #{job_script} #{gsub_options.join(' ')}"
@@ -862,17 +866,7 @@ rm -rf #{@scratch_dir} || exit 1
     save_parameters_as_tsv
     save_input_dataset_as_tsv
 
-    if SushiFabric::Application.config.fgcz?
-      # this causes sqlite3 IO error in Mac OSX (Yosemite)
-      pid = Process.fork do
-        Process.fork do
-          main
-        end # grand-child process
-      end # child process
-      Process.waitpid pid
-    else
-      main
-    end
+    main
   end
   def make_dummy_files
     dummy_files_header = []

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "1.0.1"
+  VERSION = "1.0.6"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.0.1
+  version: 1.0.6
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-11-05 00:00:00.000000000 Z
+date: 2021-02-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler