rbbt-util 5.25.35 → 5.25.36

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 5c6d0758e3a1fb39aad8fe7f3f2a077299e5f7b8
-  data.tar.gz: c03e87fa3dca241c06e1512b98d9832502a428fb
+  metadata.gz: 3cb4de42b4e6fbf447040583f2415cabed0c5f09
+  data.tar.gz: 3c71fd929873349764d6b99d973ab7a0640b44a2
 SHA512:
-  metadata.gz: cc83f79920d2738482acb2a7af927851752d5604e6ddd3961ffaca60f5e988c988fb8cb6496fb47f1f75e54f6ddc64b9aac5513e9e7daa1648413fc098151841
-  data.tar.gz: d59e75e983e285216095f902cd5cd83402a45700c31d5b8bb8c3b6acee976c723bdb46334e6cea2e2d0a80d8ddf5749b8b0989e360ee3c09ceeb9c27882ab678
+  metadata.gz: 2e5624f00564d63699a241fda887d27eb805907178a706a7a40a0b78b423282aa129bbe5b008cd09fc5983e008d5e2d16795e0bf55274888e4b408e02581ad4b
+  data.tar.gz: 2db3140abdf4fe08f4ed7190bc6cf7b2d65e2b2df10e40370187053a33a941b0e65eb25ae86dc46c5c893e55d3935f403471fc03cf9138d44e0639287d2d4b3a

data/lib/rbbt/hpc.rb

@@ -23,6 +23,7 @@ module Marenostrum
       exclusive        = options.delete :exclusive
       highmem          = options.delete :highmem
       inputs_dir       = options.delete :inputs_dir
+      config_keys      = options.delete :config_keys
 
       if contain_and_sync
         contain = "/scratch/tmp/rbbt" if contain.nil?
@@ -39,6 +40,8 @@ module Marenostrum
 
       rbbt_cmd = args.reject{|e| e == '--' }.collect{|e| e.include?(" ")? '"' + e + '"' : e } * " "
 
+      rbbt_cmd << " --config_keys='#{config_keys}'"
+
       queue = options[:queue] || 'bsc_ls'
       tasks = options[:tasks] || 1
       nodes = options[:nodes] || 1

data/lib/rbbt/persist.rb

@@ -493,6 +493,10 @@ module LocalPersist
     @local_persist_dir
   end
 
+  def local_persist_dir=(value)
+    @local_persist_dir = value
+  end
+
   def local_persist(name, type = nil, options= {}, persist_options = nil, &block)
     persist_options ||= {}
     persist_options = {:dir => local_persist_dir}.merge persist_options

data/share/rbbt_commands/stat/boxplot

@@ -0,0 +1,56 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+
+Produce a heatmap
+
+$ rbbt stat heatmap [options] <filename.tsv> [file.png]
+
+-h--help Print this help
+-w--width* Image Width
+-h--height* Image Height
+-s--size* Image Size (Height and Width)
+
+EOF
+if options[:help]
+  if defined? rbbt_usage
+    rbbt_usage 
+  else
+    puts SOPT.usage
+  end
+  exit 0
+end
+
+file, png = ARGV
+
+raise "No file" if file.nil?
+
+width, height, size, logs, positive = options.values_at :width, :height, :size, :logs, :positive
+
+size = 800 if size.nil?
+width = size if width.nil?
+height = size if height.nil?
+logs = false if logs.nil?
+positive = false if positive.nil?
+
+
+require 'rbbt/util/R'
+if png
+    R.run <<-EOF
+data = rbbt.tsv2matrix(rbbt.tsv('#{file}'))
+rbbt.png_plot('#{png}', 'boxplot(data)', width=#{ width }, height=#{ height })
+    EOF
+else
+    TmpFile.with_file(nil, :extension => 'png') do |png|
+        R.run <<-EOF
+data = rbbt.tsv2matrix(rbbt.tsv('#{file}'))
+rbbt.png_plot('#{png}', 'boxplot(data)', width=#{ width }, height=#{ height })
+        EOF
+        `eog #{png}`
+    end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.35
+  version: 5.25.36
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-03-21 00:00:00.000000000 Z
+date: 2019-03-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -360,6 +360,7 @@ files:
 - share/rbbt_commands/resource/produce
 - share/rbbt_commands/rsync
 - share/rbbt_commands/stat/abs
+- share/rbbt_commands/stat/boxplot
 - share/rbbt_commands/stat/compare_lists
 - share/rbbt_commands/stat/density
 - share/rbbt_commands/stat/heatmap