bio-pipengine 0.9.3 → 0.9.4

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data/README.md

@@ -7,6 +7,9 @@ PipEngine will generate runnable shell scripts, already configured for the PBS/T
 
 PipEngine is best suited for NGS pipelines, but it can be used for any kind of pipeline that can be runned on a job scheduling system and which is "sample" centric, i.e. you have from one side a list of samples with their corresponding raw data, and from the other side a pipeline that you would like to apply to them.
 
+PipEngine was developed to combine the typical flexibility and portability of shell scripts, with the concept of pipeline templates that can be easily applied on different input data to reproduce scientific results. The overall improvement over Makefiles or customised ad-hoc shell scripts is better readability of the pipelines using the YAML format, especially for people with no coding experience, the automated scripts generation which allows adding extra functionalities like error controls and logging directly into script jobs, and an enforced separation between the description of input data and the pipeline template, which improves clarity and reusability of analysis protocols.
+
+
 Installation
 ============
 
@@ -30,6 +33,8 @@ and then install PipEngine using RubyGems:
 gem install bio-pipengine
 ```
 
+Pipengine has been tested and should work with Ruby >= 2.1.2
+
 :: Topics ::
 ============
 
@@ -49,10 +54,11 @@ gem install bio-pipengine
 
 [PBS Options](https://github.com/bioinformatics-ptp/bioruby-pipengine#-pbs-options-)
 
+[Extending and contributing](https://github.com/bioinformatics-ptp/bioruby-pipengine#-extending-and-contributing-)
+
 :: Usage ::
 ===========
 
-PipEngine it's divided into two main sections:
 
 ```shell
 > pipengine -h
@@ -63,8 +69,6 @@ List of available commands:
 Command line for RUN mode
 -------------------------
 
-With this mode, PipEngine will submit pipeline jobs to the scheduler.
-
 **Command line**
 ```shell
 > pipenengine run -p pipeline.yml -f samples.yml -s mapping --tmp /tmp
@@ -651,7 +655,14 @@ within the job script.
 
 If a specific queue needs to be selected for sending the jobs to PBS, the ```--pbs-queue``` (short version **-q**) parameter can be used. This will pass to the ```qsub``` command the ```-q <queue name>``` taken from the command line.
 
+:: Extending and contributing ::
+================================
+
+Pipengine code is organized around main methods allowing for YAML parsing and command line arguments substitutions that are available in lib/bio/pipengine.rb. Specific logic for jobs, pipeline steps and samples is described in dedicated classes called Bio::Pipengine::Job, Bio::Pipengine::Step and Bio::Pipengine::Sample.
+
+For instance, in case the support for different schedulers needs to be introduced, it will be sufficient to modify or extend the Job.to_script method, which is the one defining scheduler-specific options in the runnable bash script.
+
 Copyright
 =========
 
-&copy;2016 Francesco Strozzi, Raoul Jean Pierre Bonnal 
+&copy;2017 Francesco Strozzi, Raoul Jean Pierre Bonnal 

data/VERSION

@@ -1 +1 @@
-0.9.3
+0.9.4

data/bin/pipengine

@@ -3,7 +3,7 @@
 $:<< File.expand_path(File.join(File.dirname(File.dirname __FILE__),"lib"))
 require 'bio-pipengine'
 
-banner_text = "\nLauncher for Complex Biological Pipelines . Copyright(C) 2013 Francesco Strozzi, Raoul Jean Pierre Bonnal\n\n" 
+banner_text = "\nLauncher for Complex Biological Pipelines . Copyright(C) 2012 Francesco Strozzi, Raoul Jean Pierre Bonnal\n\n" 
 version_text = File.read File.expand_path(File.join(File.dirname(File.dirname __FILE__),"VERSION"))
 SUB_COMMANDS = %w(run jobs)
 
@@ -46,12 +46,15 @@ when "run"
 #	end
 when "-h"
 	puts banner_text
-	puts "List of available commands:\n\trun\tSubmit pipelines to the job scheduler\n\tjobs\tShow statistics and interact with running jobs\n"
+	puts "List of available commands:\n\trun\tSubmit pipelines to the job scheduler\n"
 	exit
 else
 	global_opts = Trollop::options do
 		banner banner_text
 		version "PipEngine v#{version_text}"
+	  puts banner_text
+		puts "PipEngine v#{version_text}" 
+		puts "List of available commands:\n\trun\tSubmit pipelines to the job scheduler\n\n"
 	end
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-pipengine
 version: !ruby/object:Gem::Version
-  version: 0.9.3
+  version: 0.9.4
 platform: ruby
 authors:
 - Francesco Strozzi
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-05-09 00:00:00.000000000 Z
+date: 2017-08-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: trollop
@@ -17,28 +17,28 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 2.1.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 2.1.2
 - !ruby/object:Gem::Dependency
   name: colorize
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.8.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.8.1
 - !ruby/object:Gem::Dependency
   name: warbler
   requirement: !ruby/object:Gem::Requirement
@@ -107,7 +107,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.5
+rubygems_version: 2.6.8
 signing_key: 
 specification_version: 4
 summary: A pipeline manager