sushi_fabric 0.9.7 → 1.0.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 8ca5afb9de9e23912a2d514c547ff22d2edaf0a6c440e3663a0ac3fce59933f9
-  data.tar.gz: 7a906efa08a1bd3ee1b33dd02ff9a4350f241042626120278b720b3b3294d013
+  metadata.gz: f9006b34b7600a8d1eadd5016f972427a3b879c33773e71b73f824252c238e2c
+  data.tar.gz: 1211f6f928b02c9cb3257a000f13a57685dbabca9d947dfa8b3d3e0fea105c57
 SHA512:
-  metadata.gz: 482274611996c4e8c2d483088d1bcd8966d6136f849f7b77782d5ac0834556a56682fc2049f8c70da3aa48131bfa71ae13322a8e001252d4744d76787d9c2a23
-  data.tar.gz: 561434d611bc97fe9e30a035db0f3e3b71cbec89dc767f2531e2bf1b03905030364cf1bd833a0c432cad0d184a87a6552ae90430fe03c47f272611799d35cdea
+  metadata.gz: 8a0d8d0cee0aba783393f144ff6eaf7f22b01e5ec9e781870bec342e7ad7bdf04fa10ecd10d49f548cd010c576e606d38b76846093314a554564eafae868ec14
+  data.tar.gz: e7909f64a0328680f1fd680ec1bfed5fc852c4e64876d74eff3b113cfcddabd2baf23199d89c734344dd298bea6a44c798978788269b999be953ac0f1f531d75

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20200703-164839'
+# Version = '20201109-225541'
 
 require 'csv'
 require 'fileutils'
@@ -237,6 +237,7 @@ class SushiApp
     @params['ram'] = nil
     @params['scratch'] = nil
     @params['node'] = ''
+    @params['queue'] = ''
     @params['process_mode'] = 'SAMPLE'
     @params['samples'] = ''
     @job_ids = []
@@ -389,16 +390,18 @@ 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'
@@ -418,9 +421,17 @@ 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
@@ -447,6 +458,13 @@ 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/
@@ -794,7 +812,6 @@ 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 = "0.9.7"
+  VERSION = "1.0.2"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 0.9.7
+  version: 1.0.2
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-07-03 00:00:00.000000000 Z
+date: 2020-11-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler