sushi_fabric 1.0.0 → 1.0.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 795af5bedd1d25f2f6c41bcab16b699b015df28615ff1ef5a975f330ba8f7255
-  data.tar.gz: ebc667d556828450ae331a4e63ed07bde0b4871b97d18747bc71ff6e407f185a
+  metadata.gz: 9fdb24b4bbe247b331be53dd1a57f117e3c44dccd12a52686fc4533e17222451
+  data.tar.gz: 30b5cc93c26df8e4a5ce07196774e27d9576ec94f13f95d5286e3acbe40f8c73
 SHA512:
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-  data.tar.gz: 8a046912e3b798e662b9e1131d5a0151f36cbb83e4eb986c9827dff6e410e1910c2965d383daba7a1dc9a5798f08c566feb72bb3c812cbdcbf1f7fe9d4cf575d
+  metadata.gz: 6401d7f668742a1b66dba932c5adb70e8cf82d37da5d57cb3009798aedd32c017a2c6bc63d5a4e1fe8705b53de271c96610306f91f826d36a616e0e3ed0b1208
+  data.tar.gz: 5ac2a7cd2b3269b998f9edcf0714b91c904c51a53aecdd658d8d361c59539d6956eb4b932424e77691a38308149bf5858fef2405e88c4798738ebac4af8dccbb

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20200724-120813'
+# Version = '20210121-101344'
 
 require 'csv'
 require 'fileutils'
@@ -238,6 +238,7 @@ class SushiApp
     @params['scratch'] = nil
     @params['node'] = ''
     @params['queue'] = ''
+    @params['partition'] = ''
     @params['process_mode'] = 'SAMPLE'
     @params['samples'] = ''
     @job_ids = []
@@ -390,16 +391,18 @@ class SushiApp
     FileUtils.mkdir_p(@scratch_result_dir)
     FileUtils.mkdir_p(@job_script_dir)
   end
-  def check_latest_module_version(mod)
-    command_out =  %x[ bash -lc "source #{@module_source}; module whatis #{mod} 2>&1" ]
-    latest_mod = nil
-    command_out.split("\n").each do |line|
-      if line =~ /#{mod}/
-        latest_mod = line.split.first
-        break
+  def check_latest_modules_version(modules)
+    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
+      unless line.empty?
+        if line =~ /#{modules.join("|")}/
+          latest_modules << line
+        end
       end
     end
-    latest_mod
+    latest_modules
   end
   def job_header
     @scratch_dir = if @params['process_mode'] == 'SAMPLE'
@@ -408,8 +411,8 @@ 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
@@ -419,9 +422,17 @@ class SushiApp
                        ""
                      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(' ')}"
+                            modules_with_version = check_latest_modules_version(@modules)
+                            if @modules.length == modules_with_version.length
+                              modules_with_version.compact!
+                              "module add #{modules_with_version.join(' ')}"
+                            else
+                              @logger.error("#"*100)
+                              @logger.error("# Error in checking modules ")
+                              @logger.error("# Please check if all modules are correctly installed, searched #{@modules.join(",")} but only detected #{modules_with_version.join(",")}")
+                              @logger.error("#"*100)
+                              "exit # Please check if all modules are correctly installed, searched #{@modules.join(",")} but only detected #{modules_with_version.join(",")}"
+                            end
                           else
                             ""
                           end
@@ -484,6 +495,7 @@ 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(' ')}"
@@ -852,17 +864,7 @@ 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 = "1.0.0"
+  VERSION = "1.0.5"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.0.5
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-07-24 00:00:00.000000000 Z
+date: 2021-01-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler