rbbt-util 5.26.2 → 5.26.3

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 5ed2d44e0bb591608aab12753ff78997251b8828
+  metadata.gz: 5b582ba7448ba5e3ffcb0eac59efa4ef6a41cb90
+  data.tar.gz: 0e7144d18cc60fa26718b84949dc18bc61e318ad
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data/bin/rbbt

@@ -98,12 +98,12 @@ if mem_dump = options.delete(:dump_mem)
 end
 
 if options[:config_keys]
-  if Misc.is_filename?(options[:config_keys]) && File.exists?(options[:config_keys])
-    Rbbt::Config.load_file(options[:config_keys])
-  elsif Rbbt.etc.config_profile[options[:config_keys]].exists?
-    Rbbt::Config.load_file(Rbbt.etc.config_profile[options[:config_keys]].find)
-  else
-    options[:config_keys].split(",").each do |config|
+  options[:config_keys].split(",").each do |config|
+    if Misc.is_filename?(config) && File.exists?(config)
+      Rbbt::Config.load_file(config)
+    elsif Rbbt.etc.config_profile[config].exists?
+      Rbbt::Config.load_file(Rbbt.etc.config_profile[config].find)
+    else
       key, value, *tokens = config.split(/\s/)
       tokens = ['key:' << key << '::0'] if tokens.empty?
       tokens = tokens.collect do |tok|

data/lib/rbbt/workflow/definition.rb

@@ -71,7 +71,7 @@ module Workflow
       set_info :result_type, dep.info[:result_type]
       forget = config :forget_dep_tasks, :forget_dep_tasks, :default => FORGET_DEP_TASKS
       if forget
-        Open.ln_h dep.path, self.path
+        Open.cp dep.path, self.path
         self.dependencies = self.dependencies - [dep]
         self.set_info :dependency, dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]}
       else

data/share/rbbt_commands/workflow/task

@@ -170,6 +170,7 @@ the job dependencies recursively.
 
 -h--help Show this help
 -wd--workdir* Change the working directory of the workflow
+-wda--workdir_all* Change the working directory of ALL workflow
 -as--array_separator* Change the character that separates elements of Arrays, ',', '|', or '\\n' by default
 -fs--field_separator* Change the character that separates fields of TSV files '\\t' by default
 -jn--jobname* Job name to use. The name 'Default' is used by default
@@ -223,6 +224,8 @@ else
   remote_workflows = {}
 end
 
+Workflow.workdir = Path.setup(File.expand_path(options.delete(:workdir_all))) if options[:workdir_all]
+
 workflow = Workflow.require_workflow workflow
 
 if options[:update_all_jobs]

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.2
+  version: 5.26.3
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-04-23 00:00:00.000000000 Z
+date: 2019-04-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake