MARQ

MicroArray Rank Query (MARQ) is an application used to retrieve microarray experiments that are similar to a given query based on a rank statistic. This package includes the tools to build the microarray database, a SOAP web server to perform the queries and a merb application that offers a complete visual interface to the system with several additional features.

Installation

Quick install

rbbt_config prepare all; rbbt_config install organisms; rbbt_genecodis prepare all; rbbt_genecodis install data; marq_config prepare identifiers; marq_config prepare GEO; marq_config install GEO; marq_config prepare CustomDS; marq_config install CustomDS

Install the gem and all the dependencies. This gem depends on several others, including Rbbt. Rbbt offers an API with the gene identifier translation used in MARQ. To install MARQ follow this recipie:

  • Install Rbbt

    rbbt_config configure
    rbbt_config prepare identifiers
    rbbt_config organisms
    # Choose the organisms you are interested in, and take the keyword. Like sgd for yeast
    rbbt_config install organisms -o sgd
    
  • Install R

    • Install bioconductor and GEOquery

      source("http://bioconductor.org/biocLite.R")
      biocLite()
      biocLite('GEOquery')
      
  • Install mysql

    • Create database

      CREATE DATABASE madb;
      CREATE USER 'marq'@'localhost' IDENTIFIED BY 'marq_password';
      GRANT ALL PRIVILEGES ON madb.* TO 'marq'@'localhost';
      
  • Install MARQ

    marq_config config
    marq_config prepare identifiers
    marq_config prepare GEO
    marq_config install GEO
    
  • MARQ depends on many gems. Some may be problematic to install, in particular rsruby. You may need to get the source and build it yourself instead of using the gem command. github.com/alexgutteridge/rsruby. Also RubyInline does not work in ruby1.9 so its require has been delayed to just when its about to be used.

Note on Patches/Pull Requests

  • Fork the project.

  • Make your feature addition or bug fix.

  • Add tests for it. This is important so I don't break it in a future version unintentionally.

  • Commit, do not mess with rakefile, version, or history. (if you want to have your own version, that is fine but bump version in a commit by itself I can ignore when I pull)

  • Send me a pull request. Bonus points for topic branches.

Copyright © 2009 Miguel Vazquez. See LICENSE for details.