rbbt-util 5.21.95 → 5.21.96

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 3ec4150b254df3faaec0645421da191703778eb5
+  metadata.gz: 344b1f349d4ccc887c8d880f838de53f58d82db7
+  data.tar.gz: cc0fef8d5aa0732de3e65b912523696597701efd
 SHA512:
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+  metadata.gz: 53fc4f324fa46d7841b64fc47db959f58a9c87202de32a840e91a4ee846e124b56496fe3c3bab4e2e3d8b3ec31032ff3fe87668db6d9393b1a709459ff7db59b
+  data.tar.gz: 9ee1e9a13ca24eb82efda2b69bdf6e3a6d6b806ad3ae49b156788c316d4e6a5a0cb6050029b234db465ae8b6c9347217379fb5df17759844999cf30c29c02969

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -205,6 +205,7 @@ module TSV
       end
     end
 
+    options[:monitor] = bar
     if callback
       bar.init if bar
       exception = nil
@@ -222,7 +223,6 @@ module TSV
         raise exception if exception
       end
     else
-      options[:monitor] = bar
       TSV::Parser.traverse(io, options.merge(:monitor => bar), &block)
     end
     Log::ProgressBar.remove_bar(bar) if bar

data/lib/rbbt/tsv/parser.rb

@@ -517,7 +517,8 @@ module TSV
     end
 
     def traverse(options = {})
-      monitor, grep, invert_grep, head = Misc.process_options options, :monitor, :grep, :invert_grep, :head
+      monitor, bar, grep, invert_grep, head = Misc.process_options options, :monitor, :bar, :grep, :invert_grep, :head
+      monitor = bar if bar and monitor.nil?
       raise "No block given in TSV::Parser#traverse" unless block_given?
 
       stream = @stream
@@ -540,6 +541,7 @@ module TSV
       end
 
       progress_monitor, monitor = monitor, nil if Log::ProgressBar === monitor
+
       # setup monitor
       if monitor and (stream.respond_to?(:size) or (stream.respond_to?(:stat) and stream.stat.respond_to? :size and stream.respond_to?(:pos)))
         size = case

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

@@ -311,7 +311,7 @@ module Misc
     parts = line.split(sep, -1)
     chr, start, eend, *rest = parts
     start = start.to_i
-    if eend =~ /^\d+$/
+    if eend =~ /^\d+(\t.*)?$/
       eend = eend.to_i
     else
       eend = start.to_i

data/lib/rbbt/workflow/accessor.rb

@@ -766,6 +766,7 @@ module Workflow
                        compute = nil
                      end
 
+                     options = IndiferentHash.setup(options.dup)
                      dep = dependency.call jobname, options.merge(_inputs), real_dependencies
 
                      dep = [dep] unless Array === dep
@@ -781,6 +782,7 @@ module Workflow
                      }
                      dep = new_
                    else
+                     _inputs = IndiferentHash.setup(_inputs.dup)
                      dep = dependency.call jobname, _inputs, real_dependencies
                      if Hash === dep
                        inputs = assign_dep_inputs({}, dep[:inputs], real_dependencies, dep[:workflow].task_info(dep[:task]))

data/share/Rlib/util.R

@@ -477,7 +477,7 @@ rbbt.png_plot <- function(filename, p, width=500, height=500, ...){
     eval(parse(text=p));
 }
 
-rbbt.heatmap <- function(filename, data, width=500, height=500, take_log=FALSE, ...){
+rbbt.heatmap <- function(filename, data, width=500, height=500, take_log=FALSE, stdize=TRUE, ...){
     opar = par()
     png(filename=filename, width=width, height=height);
 
@@ -500,7 +500,10 @@ rbbt.heatmap <- function(filename, data, width=500, height=500, take_log=FALSE,
     }
 
     rbbt.require('pls')
-    data = stdize(data)
+
+    if (stdize){
+        data = stdize(data)
+    }
 
     heatmap.2(data, scale='column', ...)
 

data/share/rbbt_commands/app/start

@@ -41,7 +41,7 @@ end
 options[:Port] = options["port"]
 options[:server] = options["server"]
 options[:Host] = options["Host"]
-options[:Bind = options["Bind"]
+options[:Bind] = options["Bind"]
 
 options[:Host] ||= "0.0.0.0"
 options[:Bind] ||= "0.0.0.0"

data/share/rbbt_commands/workflow/install

@@ -31,7 +31,7 @@ if options[:help]
 end
 
 workflow = ARGV[0]
-repo = ARGV[1]
+base_repo = ARGV[1]
 
 raise "No workflow specified" if workflow.nil?
 
@@ -61,8 +61,17 @@ Misc.in_dir(workflow_dir) do
       end
     else
       Log.info "Installing: " + workflow
-      if repo.nil?
+
+      if base_repo.nil?
         repo_base_url = Rbbt.etc.workflow_repo.exists? ? Rbbt.etc.workflow_repo.read.strip : 'https://github.com/Rbbt-Workflows/'
+      else
+        repo_base_url = base_repo
+      end
+
+
+      if repo_base_url.include?(workflow) or repo_base_url.include?(Misc.snake_case(workflow))
+        repo = repo_base_url
+      else
         begin
           repo = File.join(repo_base_url, workflow + '.git')
           CMD.cmd("wget '#{repo}' -O /dev/null").read
@@ -76,6 +85,7 @@ Misc.in_dir(workflow_dir) do
           end
         end
       end
+
       Log.warn "Cloning #{ repo }"
       Misc.insist do
         `git clone "#{repo}" #{ Misc.snake_case(workflow) }`

data/share/rbbt_commands/workflow/list

@@ -13,7 +13,7 @@ Path.setup(workflow_dir) unless Path === workflow_dir
 workflows = Workflow.installed_workflows
 
 if options[:describe]
-  workflows.each do |workflow|
+  workflows.sort.each do |workflow|
     Workflow.require_workflow workflow
     workflow = Workflow.workflows.select{|w| Misc.camel_case(w.to_s) == Misc.camel_case(workflow)}.first
     puts "# "<<[Misc.camel_case(workflow.to_s), workflow.description] * ": "
@@ -24,7 +24,7 @@ if options[:describe]
 
   end
 else
-  workflows.each do |workflow|
+  workflows.sort.each do |workflow|
     puts Misc.camel_case(workflow.to_s)
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.95
+  version: 5.21.96
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-08-30 00:00:00.000000000 Z
+date: 2017-09-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake