rput 0.1.1 → 0.1.2

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

data/lib/starter.rb

@@ -9,9 +9,7 @@ class CycleController
   def initialize(opts)
     @opts = opts
     @opts[:num_ptrees] ||= @opts[:num_parsi_trees]
-    @script = "raxml_batch_cycle.sh"
     @numtaxa, @seqlen  = File.open(@opts[:phy]).readlines.first.split.map{|w| w.to_i}
-    raise "#{@script} missing" unless File.exist?(@script)
   end
   def parsimonator_requirements
    bytes_inner =  @numtaxa.to_f * @seqlen.to_f
@@ -30,7 +28,8 @@ class CycleController
    puts required_MB
    required_MB.to_i.to_s
   end
-  def run_as_batch
+  def run_as_batch(script)
+    raise "#{script} missing" unless File.exist?(script)
     raise "User Number of parsimony trees not set" unless @opts[:num_parsi_trees] > 0
     raise "Total Number of parsimony trees not set" unless @opts[:num_ptrees] > 0
     opts = @opts[:iter].to_s
@@ -42,15 +41,15 @@ class CycleController
     opts += " " + @opts[:num_bestML_trees].to_s
     opts += " " + @opts[:exp_name].to_s
     opts += " " + @opts[:base_dir].to_s
-    puts "./#{@script} #{opts}"
-    system "./#{@script} #{opts}"
+    puts "./#{script} #{opts}"
+    system "./#{script} #{opts}"
   end
 end
 
 class TreeBunchStarter 
   # Given an initial alignment, it creates a initial bunch of ML trees in bunch_0 dir
   # should log results
-  attr_reader :cluster
+  attr_reader :cluster_batch
   def initialize(opts)
     @phylip = opts[:phylip]
     @base_dir = opts[:base_dir]
@@ -72,7 +71,7 @@ class TreeBunchStarter
     @CAT_topology_bunch_order = File.join @ml_trees_dir, "CAT_topology_bunch_order.txt"
     @bestML_bunch = File.join @bestML_trees_dir, "best_bunch.nw"
     @prev_bestML_bunch = File.join @prev_dir, "best_ml_trees", "best_bunch.nw" unless @prev_dir.nil?
-    @cluster = opts[:cluster] || false 
+    @cluster_batch = opts[:cluster_batch] 
   end
   def logput(msg, error = false)
     @logger ||= Logger.new(File.join @base_dir, "starter.log")
@@ -116,17 +115,17 @@ class TreeBunchStarter
       if num_bestML_trees > num_parsi_trees * prev_trees.size
         raise "#bestML trees (#{num_bestML_trees}) is too higher than trees from previous round"
       end
-      if @cluster
+      unless @cluster_batch.empty?
         logput "Exp #{opts[:exp_name]}, your cluster will take care of this update no #{@update_id}. stay tuned"
               c = CycleController.new(:iter => @update_id, 
-				      :phy => @phylip_updated, 
+				                              :phy => @phylip_updated, 
                                       :num_parsi_trees => num_parsi_trees, 
                                       :num_ptrees => num_parsi_trees * prev_trees.size, 
                                       :num_bestML_trees => num_bestML_trees,
                                       :base_dir => @base_dir,
                                       :exp_name => opts[:exp_name]
                                      )
-              c.run_as_batch
+              c.run_as_batch(@cluster_batch)
         "cluster"
       else
         logput "****** Start update no #{@update_id} ********"
@@ -173,16 +172,16 @@ class TreeBunchStarter
         raise "#bestML trees (#{num_bestML_trees}) cant be higher than #parsi trees(#{num_parsi_trees})"
       end
       # phases 2 and 3 can be done in paralell
-      if @cluster 
+      unless @cluster_batch.empty?
               logput "your cluster will take care of this start #{@update_id}. Stay tuned"
               c = CycleController.new(:iter => 0, 
-				      :phy => @phylip, 
+                                      :phy => @phylip, 
                                       :num_parsi_trees => num_parsi_trees, 
                                       :num_bestML_trees => num_bestML_trees,
                                       :base_dir => @base_dir,
                                       :exp_name => opts[:exp_name]
                                      )
-              c.run_as_batch
+              c.run_as_batch(@cluster_batch)
               "cluster"
       else
 	      logput "Start generating initial bunch"
@@ -204,7 +203,7 @@ class TreeBunchStarter
   end
   private
     def check_options(opts)
-      supported_opts = [:num_parsi_trees, :num_bestML_trees, :exp_name]
+      supported_opts = [:num_parsi_trees, :num_bestML_trees, :exp_name, :cycle_batch_script]
       opts.keys.each do |key|
         unless supported_opts.include?(key)
           logput "Option #{key} is unknwon"

data/rput.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{rput}
-  s.version = "0.1.1"
+  s.version = "0.1.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = [%q{Fernando Izquierdo-Carrasco}]
-  s.date = %q{2012-03-29}
+  s.date = %q{2012-04-03}
   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: 25
+  hash: 31
   prerelease: 
   segments: 
   - 0
   - 1
-  - 1
-  version: 0.1.1
+  - 2
+  version: 0.1.2
 platform: ruby
 authors: 
 - Fernando Izquierdo-Carrasco
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-03-29 00:00:00 Z
+date: 2012-04-03 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   type: :development