sushi_fabric 0.9.9 → 1.0.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: b68363a7da5c166ab7c38d8310b9d151ce490a1d3d4f6d48bdfa5a3484c0abf1
+  metadata.gz: 3a9c780f513fc42be122da7a0cb97e5e8c4a70e84af98ea746964a5b7853f1c5
+  data.tar.gz: 4d14ca10808dbee2401088cc885d77ac2c4040ca73a984993f833b42d049ade8
 SHA512:
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-  data.tar.gz: b936c6a57a6683b1a19874627eb9bc4ba1719d0664f85794e4ee9d0face5eba3d424e06fd60158afbb53dc9b3b1c9b1330e94fdacdc17262f64ed1fdd1310eac
+  metadata.gz: 8639f58865956062ecd97f269dd426c2674ada7d602850520b323370150b50e99cfed4a5a60e67fa001fbd9035a806a4ef426f1b7db03fb5312a0fa5d36a412e
+  data.tar.gz: 0d2f463786f8397c73cba8026cd2b1ac0f4a1fbda5252ca598c39f4aaf81d25c1d6d6c9020739f2c31ecee59857ee5d09ace1f4f9a1aa675694c4cf932273b59

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20200724-111508'
+# Version = '20210115-105702'
 
 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'
@@ -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
@@ -448,6 +459,13 @@ cd $SCRATCH_DIR || exit 1
   end
   def job_footer
     @out.print "#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP\n"
+    if File.exist?("/usr/local/ngseq/miniconda3/etc/profile.d/conda.sh")
+      @out.print <<-EOS
+. "/usr/local/ngseq/miniconda3/etc/profile.d/conda.sh"
+conda activate sushi
+      EOS
+    end
+
     if @output_files
       @output_files.map{|header| next_dataset[header]}.each do |file|
         # in actual case, to save under /srv/gstore/
@@ -477,6 +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(' ')}"
@@ -845,17 +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 = "0.9.9"
+  VERSION = "1.0.4"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 0.9.9
+  version: 1.0.4
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-07-24 00:00:00.000000000 Z
+date: 2021-01-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler