sushi_fabric 1.0.2 → 1.0.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f9006b34b7600a8d1eadd5016f972427a3b879c33773e71b73f824252c238e2c
-  data.tar.gz: 1211f6f928b02c9cb3257a000f13a57685dbabca9d947dfa8b3d3e0fea105c57
+  metadata.gz: 437c1a17818ce1c691886fface6c5395eae69d72024f542eb6497885814d7b82
+  data.tar.gz: d08bf18f1fd4d58285df67b682e134951afa6325a6192097b3ecd7b0d8f3b823
 SHA512:
-  metadata.gz: 8a0d8d0cee0aba783393f144ff6eaf7f22b01e5ec9e781870bec342e7ad7bdf04fa10ecd10d49f548cd010c576e606d38b76846093314a554564eafae868ec14
-  data.tar.gz: e7909f64a0328680f1fd680ec1bfed5fc852c4e64876d74eff3b113cfcddabd2baf23199d89c734344dd298bea6a44c798978788269b999be953ac0f1f531d75
+  metadata.gz: ab3b854e32de48cfe000dc4d524a3fb6a3998ca60b23ee3754f10755faee45b9e5c50de6d37e2ab48e91f3dbea415eb8675c4b30256bed7df297fac6ab98860f
+  data.tar.gz: 5b4ddc75fe749426e0765e5bca55fc41003387e46d9ac53317c1462552c71d5f82efebb3b93166128efd9e7a2784460ec4a1146eb77cd1314b25319cabfbfb96

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20201109-225541'
+# Version = '20210211-145021'
 
 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 = []
@@ -409,12 +412,11 @@ class SushiApp
                    else
                      @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}"
-                              else
-                                ''
-                              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? and parent_data_set_job_ids = parent_data_set.jobs.map{|job| job.submit_job_id} and !parent_data_set_job_ids.join.empty?
+                        "#SBATCH --dependency=afterany:#{parent_data_set_job_ids.join(":")}"
+                      else
+                        ''
+                      end
     module_src_command = if @module_source and @modules and !@modules.empty?
                        "source #{@module_source}"
                      else
@@ -494,6 +496,7 @@ 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 +865,7 @@ 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 = "1.0.2"
+  VERSION = "1.0.7"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.0.2
+  version: 1.0.7
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-11-09 00:00:00.000000000 Z
+date: 2021-02-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler