Jeff Shantz jsuwo

Working with Ruby on the MC 10 systems

While it is possible to install Ruby on a system-wide basis, it is much more common amongst the Ruby community to use a tool called rvm (Ruby Version Manager) to build and install Ruby and to manage the installation of Ruby gems (libraries). This tutorial will get you started with RVM on the MC 10 systems.

Prerequisites

This tutorial assumes:

You are working on one of the Linux systems in MC 10. Do not attempt this on obelix.
You have at least 100 - 200 MB of free space in your GAUL account, depending on the Ruby gems that you install. You have at least 1 GB of quota, so this shouldn't be much of a hardship for you. If you need more quota to make this work, contact Jeff at [x@y, where x = jeff, y = csd.uwo.ca].

$ cat test.xml | ruby -e "puts ARGF.read.scan(/<article-title>(.*?)<\/article-title>/m).flatten.map { |title| title.gsub(/\s+/, ' ') }" | wc -l 

      78

$ cat test.xml | ruby -e "puts ARGF.read.scan(/<article-title>(.*?)<\/article-title>/m).flatten.map { |title| title.gsub(/\s+/, ' ') }"

Chemical Approaches To Perturb, Profile, and Perceive Glycans
On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database
Annotation of glycoproteins in the SWISS-PROT database

$ cat test.xml | ruby -r nokogiri -e "puts Nokogiri::XML(ARGF.read).xpath('//article-title').map { |t| t.content.gsub(/\s+/, ' ') }" | wc -l

      78
      
$ cat test.xml | ruby -r nokogiri -e "puts Nokogiri::XML(ARGF.read).xpath('//article-title').map { |t| t.content.gsub(/\s+/, ' ') }"

Chemical Approaches To Perturb, Profile, and Perceive Glycans
On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database
Annotation of glycoproteins in the SWISS-PROT database

	*PPD-Adobe: "4.3"
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	*PPD-Adobe: "4.3"
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	*PPD-Adobe: "4.3"

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	# This script can be run using any of the following:
	#
	# ruby RegexMatchingExampleExplained.rb < file1.xml
	# cat file1.xml file2.xml file3.xml \| ruby RegexMatchingExampleExplained.rb
	# ruby RegexMatchingExampleExplained.rb file1.xml file2.xml file3.xml
	#

	# Read everything from standard input or from files specified as command line arguments
	content = ARGF.read