sushi_fabric 0.9.8 → 1.0.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 7ff6d22fd4617f2e10459474d86f706b1f4bbd39c7922031271c49c8f4f45269
+  metadata.gz: b645fb8369eee1152493ef424f092cd00f0a5a08c27cb78d4b081e17c0b18784
+  data.tar.gz: 2630d702479d4eac533f737e226c80cbe115598d891eb526ec1f8e7004fc9481
 SHA512:
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-  data.tar.gz: eacc4d03b02f4a94adeb42a40f2217022aa0b7659c1cfe3fc1035d9726dd04375e15eebf47c4a7f582416c7c7b18eabaac4e9c8b6e46c5c48fbea4139380ada6
+  metadata.gz: a68e3cee864cc0cd12b5335b9d8d1eb8688175870455b61d4153109c8d98e5d77846d4ef87d50bec8c1dde624511cfde6b60de1110724b1878ccc19af91bd6ea
+  data.tar.gz: 331228ad3cebe41dbf0b6b921e2284d1030e2948f92b2ecebbc9955242ec3c47730b972e367947018114748e0fe9c65a6f9e3660896047684370b3f8fabfd8c5

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20200723-132451'
+# Version = '20201218-155451'
 
 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(' ')}"
@@ -795,7 +814,6 @@ rm -rf #{@scratch_dir} || exit 1
             if next_dataset.workunit_id
               @job_scripts.each do |job_script|
                 open(job_script, "a") do |out|
-                  out.puts "module load Dev/Python"
                   out.puts "WORKUNIT_ID=#{next_dataset.workunit_id}"
                   out.puts "update_resource_size -w $WORKUNIT_ID"
                 end

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "0.9.8"
+  VERSION = "1.0.3"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 0.9.8
+  version: 1.0.3
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-07-23 00:00:00.000000000 Z
+date: 2020-12-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler