sushi_fabric 1.0.0 → 1.0.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 795af5bedd1d25f2f6c41bcab16b699b015df28615ff1ef5a975f330ba8f7255
-  data.tar.gz: ebc667d556828450ae331a4e63ed07bde0b4871b97d18747bc71ff6e407f185a
+  metadata.gz: 6bb6ed61655c7decac6439f7bd3c73784888ae9686d2611c10f9d4c40bda0621
+  data.tar.gz: 91e98688ac53cfc55560decb2537ee1b38e9c93d24ffb4cfae02875088e2e910
 SHA512:
-  metadata.gz: 6ae60c4d4acef1444c9b1bfdb11f2dc6455add3414cfc63412603051d992c402c67037c45ff136b905ac2166100e36fa3f1e3c8d313cea80bc24c31a3b7f2577
-  data.tar.gz: 8a046912e3b798e662b9e1131d5a0151f36cbb83e4eb986c9827dff6e410e1910c2965d383daba7a1dc9a5798f08c566feb72bb3c812cbdcbf1f7fe9d4cf575d
+  metadata.gz: d2ffd594a92358285b0996f0fa06053af38cb65cfe337049b0e619f7e590fdd8ae91b005adfa50c088ced30b7c8235dd7f6d469f36284af62e5a94f5bab7d4b7
+  data.tar.gz: b5ee9600a1e1b2fe1d76b27bc37cc30a230a5cafb0e613fb5ab13f587ddade33e8f365c87be81e315239d78fb90c99bffe9f65d5ede95f62c8947c1c540be75a

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20200724-120813'
+# Version = '20201105-115625'
 
 require 'csv'
 require 'fileutils'
@@ -390,16 +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 " " | sort | 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 +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

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "1.0.0"
+  VERSION = "1.0.1"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.0.1
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-07-24 00:00:00.000000000 Z
+date: 2020-11-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler