workflow_manager 0.8.0 → 0.9.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile.lock

@@ -1,25 +1,26 @@
 PATH
   remote: .
   specs:
-    workflow_manager (0.7.9)
+    workflow_manager (0.8.1)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    concurrent-ruby (1.2.0)
-    connection_pool (2.3.0)
-    rack (3.0.4.1)
-    redis (5.0.6)
-      redis-client (>= 0.9.0)
-    redis-client (0.12.1)
+    concurrent-ruby (1.2.3)
+    connection_pool (2.4.1)
+    rack (3.0.9)
+    redis (5.0.8)
+      redis-client (>= 0.17.0)
+    redis-client (0.19.1)
       connection_pool
-    sidekiq (7.0.5)
+    sidekiq (7.2.1)
       concurrent-ruby (< 2)
       connection_pool (>= 2.3.0)
       rack (>= 2.2.4)
-      redis-client (>= 0.11.0)
+      redis-client (>= 0.19.0)
 
 PLATFORMS
+  ruby
   x86_64-linux
 
 DEPENDENCIES
@@ -28,4 +29,4 @@ DEPENDENCIES
   workflow_manager!
 
 BUNDLED WITH
-   2.3.26
+   2.5.5

data/lib/workflow_manager/cluster.rb

@@ -28,7 +28,7 @@ module WorkflowManager
     end
     def job_pending?(job_id)
     end
-    def copy_commands(org_dir, dest_parent_dir, now=nil)
+    def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
     end
     def kill_command(job_id)
     end
@@ -75,7 +75,7 @@ module WorkflowManager
       result = `#{command}`
       result.to_s.empty? ? false : true
     end
-    def copy_commands(org_dir, dest_parent_dir, now=nil)
+    def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
       commands = []
       commands << "mkdir -p #{dest_parent_dir}"
       commands << "cp -r #{org_dir} #{dest_parent_dir}"
@@ -199,7 +199,7 @@ module WorkflowManager
       end
       qstat_flag
     end
-    def copy_commands(org_dir, dest_parent_dir, now=nil)
+    def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
       commands = if now == "force"
                    target_file = File.join(dest_parent_dir, File.basename(org_dir))
                    ["g-req copynow -f #{org_dir} #{dest_parent_dir}"]
@@ -300,7 +300,7 @@ module WorkflowManager
   end
 
   class FGCZCourseCluster < FGCZCluster
-    def copy_commands(org_dir, dest_parent_dir, now=nil)
+    def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
       commands = ["cp -r #{org_dir} #{dest_parent_dir}"]
     end
     def delete_command(target)
@@ -333,7 +333,7 @@ module WorkflowManager
     def job_pending?(job_id)
       # TODO
     end
-    def copy_commands(org_dir, dest_parent_dir, now=nil)
+    def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
       # TODO
     end
     def kill_command(job_id)
@@ -411,7 +411,7 @@ module WorkflowManager
       end
       qstat_flag
     end
-    def copy_commands(org_dir, dest_parent_dir, now=nil)
+    def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
       commands = if now == "force"
                    target_file = File.join(dest_parent_dir, File.basename(org_dir))
                    ["g-req copynow -f #{org_dir} #{dest_parent_dir}"]
@@ -521,14 +521,16 @@ module WorkflowManager
       end
       qstat_flag
     end
-    def copy_commands(org_dir, dest_parent_dir, now=nil)
+    def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
       commands = if now == "force"
                    target_file = File.join(dest_parent_dir, File.basename(org_dir))
                    ["g-req copynow -f #{org_dir} #{dest_parent_dir}"]
                  elsif now
                    ["g-req copynow #{org_dir} #{dest_parent_dir}"]
-                 else
+                 elsif queue.nil? or queue == "light"
                    ["g-req -w copy #{org_dir} #{dest_parent_dir}"]
+                 else
+                   ["g-req -w copy -f heavy #{org_dir} #{dest_parent_dir}"]
                  end
     end
     def kill_command(job_id)
@@ -546,7 +548,7 @@ module WorkflowManager
   end
 
   class FGCZDebian10DemoCluster < FGCZDebian10Cluster
-    def copy_commands(org_dir, dest_parent_dir, now=nil)
+    def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
       commands = ["cp -r #{org_dir} #{dest_parent_dir}"]
     end
     def delete_command(target)

data/lib/workflow_manager/server.rb

@@ -202,8 +202,8 @@ module WorkflowManager
     def hello
       'hello hoge hoge bar boo bundle, '+ @cluster.name
     end
-    def copy_commands(org_dir, dest_parent_dir, now=nil)
-      @cluster.copy_commands(org_dir, dest_parent_dir, now)
+    def copy_commands(org_dir, dest_parent_dir, now=nil, queue="light")
+      @cluster.copy_commands(org_dir, dest_parent_dir, now, queue)
     end
     def kill_job(job_id)
       status(job_id, 'FAIL')

data/lib/workflow_manager/version.rb

@@ -1,3 +1,3 @@
 module WorkflowManager
-  VERSION = "0.8.0"
+  VERSION = "0.9.0"
 end

data/start_workflow_manager.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/bash
 source /usr/local/ngseq/etc/lmod_profile
-module load Dev/Ruby/3.1.3
-module load Tools/Redis/7.0.8
+module load Dev/Ruby/3.2.3
+module load Tools/Redis/7.2.4
+. "/usr/local/ngseq/miniconda3/etc/profile.d/conda.sh"
 conda activate gtools_env
 which python
 which g-sub

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: workflow_manager
 version: !ruby/object:Gem::Version
-  version: 0.8.0
+  version: 0.9.0
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-02-17 00:00:00.000000000 Z
+date: 2024-02-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -98,7 +98,7 @@ homepage: ''
 licenses:
 - MIT
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -113,8 +113,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.26
-signing_key:
+rubygems_version: 3.5.5
+signing_key: 
 specification_version: 4
 summary: Workflow Manager manages job submissions using dRuby.
 test_files: