Sunday, April 13, 2014

Inability to bundle install due to certificate error

ERROR: cannot verify rubygems.orgs certificate, issued by a/C=US/O=GeoTrust, Inc./CN=RapidSSL CA. Unable to locally verify the issuers authority.


[LINUX_SERVER]# openssl s_client -host rubygems.org -port 443
socket: Connection refused
connect:errno=111

-à Here ideally the certificate should be visible.

[LINUX_SERVER]# ruby -ropenssl -e 'p OpenSSL::OPENSSL_VERSION'
"OpenSSL 1.0.0 29 Mar 2010"


Following are the commands to install/update openssl:
1.      rvm pkg install openssl
2.      rvm reinstall all —force —with-openssl-dir=$rvm_path/usr

This usually occurs if you are behind a firewall

export http_proxy= à will allow the installation behind a firewall.

For the openssl hearbleed issues, can google out and go through the various security patches.
Posting fe below:

1. http://lifehacker.com/what-the-heartbleed-security-bug-means-for-you-1560801201
2. http://www.hak9.com/fix-heart-bleed-bug-centos-ubuntu/


Saturday, April 12, 2014

Installing Ruby in Linux behind a firewall or where you don't root access


Ok, so the topic can be found very easy! But how will you be installing in a linux box, in which you don’t have root/admin access, and/or ports are blocked by firewall.

  1. Install WinScp
  2. Connect to the linux box
  3. Transfer the .gem files downloaded from gem repository, to the linux box


[doel@MY_LINUX_SERVER~]$ gem install rails --local /home/doel/rails-4.0.2.gem
ERROR:  While executing gem ... (Gem::DependencyError)
Unable to resolve dependencies: sprockets-rails requires sprockets (~> 2.8); railties requires thor (< 2.0, >= 0.18.1); actionmailer requires mail (~> 2.5.4); activerecord requires arel (~> 4.0.0), activerecord-deprecated_finders (~> 1.0.2); activemodel requires builder (~> 3.1.0); actionpack requires builder (~> 3.1.0), rack-test (~> 0.6.2), erubis (~> 2.7.0); activesupport requires i18n (>= 0.6.4, ~> 0.6), multi_json (~> 1.3), tzinfo (~> 0.3.37), thread_safe (~> 0.1)

In order to install all the dependencies, you need to install all the gem one by one.Though it's a laborious task, but unless you are getting admin/root access it's another workaround.

Saturday, December 14, 2013

Bioruby...presentation in RubyConf Miami 2013



"Bioruby"...understanding the intricacies of 'Life' using Ruby

Learn about the genes, which controls everything you do and find out how you can ease the task of your similarity with a salamander using Bioruby!
Bioruby is great Bioinformatics tool which helps to process biological data and analyze it. 5 years after ruby programming language came into vogue(1995), bioruby came into existence in 2000, both developed in Japan. BioRuby project provides an integrated environment in bioinformatics for the Ruby language. This project is supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation.Welcome to the ruby in the living world, integrating ruby with the Bioinformatics and have fun.
On one hand we have the Bioinformatics, the large database of the huge genome sequences, the search algorithms to search the gene similarity between different organisms, gene-mutations using the popular search tool Blast, Fasta etc. BioRuby helps us to do the same searching thing using ruby programming language. As ruby is a pure object-oriented programming language(everything in ruby is an object) and being a easy to read and write, it's fun to use here without being lost in the plethora of genomic data.
One of the greatest contributions from Bioruby is Biogems, which like any other rubygems helps to perform modular approaches in order to perform specific functionality. One such gem is bio-ucsc-api gem, which helps to fetch record from UCSC DB and the best part is the gem has been implemented using the Actice Record Framework thereby easing the record fetch, instead of complex sql queries. We explained the basic concepts of Gene, DNA. RNA, Amino-acids, Human Genome Project and how these huge data are stored and analyzed by the famous Bioinformatics tools like BLAST, Fasta and how Bioruby interacts with the different biological databases like Genbank, Swissprot etc.