rbbt-util 5.26.14 → 5.26.15

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 7d7a28e6a943f395d31b6f9704678c14baf4d868760bd58c55e7db3c004fb5c5
-  data.tar.gz: 25a26a4c39469b372daca3868310d11a0a755b5e0fc49856e574d80129819017
+  metadata.gz: 4ca1b6e54187f2a185a4808e193c8a7edf119c727ebd458a43de22c2ce459dbe
+  data.tar.gz: df37635156a96711ac3a17eb92ec342200d37561a24af7c159ef947f3b0b4520
 SHA512:
-  metadata.gz: cfe636c2eeed2368efc8b3ca1cbf83aec58af126e887d13be843d8da8e42e3ff7eae96d5ab3b22515d1b29f04ac229b26edefbb6b23968529ec8978f0df75aa3
-  data.tar.gz: c8694b64f5f79cabcf7f7c588fc9733fc999505fa66dbf7c706e0e0dc2d533873ffd60a11614edd60b5a9b344c819621d4928117c050134a688139c202a26609
+  metadata.gz: d0f65a81a0bb09e76ed0dbb7460a3d3703d4bc4df4f1486ae40fec511b0fb931ea9d35b0db468a2ee8d266af367ca42ed61522c4b04c730b824695ecbf9bfb7c
+  data.tar.gz: 4265b0702cf71164fc828a8cc60c98c032be79734d0aa93f0b694d5698c82d89e599cab0456458aa778a649946e71da151c6a8888fa54ab85732b749b9844beb

data/lib/rbbt/hpc.rb

@@ -120,6 +120,11 @@ mkdir -p "$SINGULARITY_RUBY_INLINE"
 # Prepare container dir
 CONTAINER_DIR="#{contain}"
 mkdir -p $CONTAINER_DIR/.rbbt/etc/
+
+for dir in .ruby_inline git scratch home projects; do
+    mkdir -p $CONTAINER_DIR/$dir
+done
+
 for tmpd in persist_locks  produce_locks  R_sockets  sensiblewrite  sensiblewrite_locks  step_info_locks  tsv_open_locks; do
     mkdir -p $CONTAINER_DIR/.rbbt/tmp/$tmpd
 done

data/lib/rbbt/util/cmd.rb

@@ -4,6 +4,14 @@ require 'open3'
 
 module CMD
 
+  def self.gzip_pipe(file)
+    Open.gzip?(file) ? "<(gunzip -c '#{file}')" : "'#{file}'"
+  end
+
+  def self.bash(cmd)
+    %Q(bash <<EOF\n#{cmd}\nEOF\n)
+  end
+
   def self.process_cmd_options(options = {})
     string = ""
     options.each do |option, value|

data/lib/rbbt/util/misc/omics.rb

@@ -179,18 +179,24 @@ module Misc
         "-" * (ref.length - m.length)
       when (ref.length == 1 and m.length == 1)
         m
+      when (ref == m)
+        nil
       else
         if ref == '-'
           res = '+' + m
         else
-          res = '-' * ref.length
-          res << m unless m == '-'
+          if ref[0] == m[0]
+            res = '+' << m[1..-1]
+          else
+            res = '-' * ref.length
+            res << m unless m == '-'
+          end
         end
         Log.debug{"Non-standard annotation: #{[ref, m]} (#{ muts }) => #{ res }"}
 
         res
       end
-    end
+    end.compact
 
     [pos, muts]
   end

data/lib/rbbt/workflow.rb

@@ -213,6 +213,15 @@ module Workflow
                   end
   end
 
+  def import_task(workflow, orig, new)
+    new_task = workflow.tasks[orig].clone
+    new_task.workflow = self
+    new_task.name = new
+    tasks[new] = new_task
+    task_dependencies[new] = workflow.task_dependencies[orig]
+    task_description[new] = workflow.task_description[orig]
+  end
+
   def workdir=(path)
     path = Path.setup path.dup unless Path === path
     @workdir = path

data/lib/rbbt/workflow/definition.rb

@@ -67,6 +67,7 @@ module Workflow
   def dep_task(name, *dependency, &block)
     dep(*dependency, &block)
     task name do
+      raise RbbtException, "dependency not found in dep_task" if dependencies.empty?
       dep = dependencies.last.join
       set_info :result_type, dep.info[:result_type]
       forget = config :forget_dep_tasks, :forget_dep_tasks, :default => FORGET_DEP_TASKS

data/test/rbbt/util/test_cmd.rb

@@ -75,4 +75,7 @@ line33
     end
   end
 
+  def test_bash
+    puts CMD.bash("awk 'test'")
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.14
+  version: 5.26.15
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-05-30 00:00:00.000000000 Z
+date: 2019-05-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake