rput 0.1.2 → 0.1.3

data/VERSION

@@ -1 +1 @@
-0.1.2
+0.1.3

data/lib/starter.rb

@@ -42,7 +42,7 @@ class CycleController
     opts += " " + @opts[:exp_name].to_s
     opts += " " + @opts[:base_dir].to_s
     puts "./#{script} #{opts}"
-    system "./#{script} #{opts}"
+    system "./#{script} #{opts} > #{File.join @base_dir, "starter.log")}"
   end
 end
 
@@ -110,6 +110,8 @@ class TreeBunchStarter
       # prepare the parsimony starting trees
       raise "prev bunch not ready #{@prev_bestML_bunch}" unless File.exist?(@prev_bestML_bunch)
       last_best_bunch = NewickFile.new(@prev_bestML_bunch)
+      # TODO this save_each_newick_as should be wrapped around sth. that considers a list of outliers and
+      # prunes out the ouliers before saving as "prev_parsi_tree" to make it compatible with the next round
       last_best_bunch.save_each_newick_as(File.join(@parsimony_trees_dir, 'prev_parsi_tree'), "nw") 
       prev_trees = Dir.entries(@parsimony_trees_dir).select{|f| f =~ /^prev_parsi_tree/}
       if num_bestML_trees > num_parsi_trees * prev_trees.size

data/rput.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{rput}
-  s.version = "0.1.2"
+  s.version = "0.1.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = [%q{Fernando Izquierdo-Carrasco}]
-  s.date = %q{2012-04-03}
+  s.date = %q{2012-04-13}
   s.description = %q{Automated iterations of raxml runs over externally-extended phylip files}
   s.email = %q{fer.izquierdo@gmail.com}
   s.extra_rdoc_files = [

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rput
 version: !ruby/object:Gem::Version 
-  hash: 31
+  hash: 29
   prerelease: 
   segments: 
   - 0
   - 1
-  - 2
-  version: 0.1.2
+  - 3
+  version: 0.1.3
 platform: ruby
 authors: 
 - Fernando Izquierdo-Carrasco
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-04-03 00:00:00 Z
+date: 2012-04-13 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   type: :development