INSTALL.txt

======
Source
======

The development version of Grape is available here:

https://github.com/rna-seq/grape.buildout.git

========
Releases
========

Grape software packages are available from the Grape home page:

http://big.crg.cat/services/grape

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Install
=======

After downloading the package, unpack it:

tar xfvz grape.buildout-1.9.5.tar.gz
cd grape.buildout-1.9.5

If you want to test Grape with your own test dataset, go to the Quick pipeline
folder:

    cd pipelines/Quick

Then follow the README.txt

If you want to test Grape with a minimal test dataset, go to the Test pipeline
folder:

    cd pipelines/Test

Then follow the README.txt

If you want to install the Grape web server, go the the devel server folder:

    cd servers/devel

Then follow the README.txt

============
Dependencies
============

You need to have access to a MySQL database.

    MySQL
        - 5.1.45 or above

Make sure to have the following standard programming languages installed:

    Perl 
        - 5.10.1 or above
    Java 
        - A Java 1.6 compliant runtime environment is necessary.
          It is recommended to employ the most recent Java Runtime Environment 
          (JRE) available from the traditional Java project:
          http://java.com/en/download/index.jsp
    R
        - 2.13.0 or above
    Python
        - 2.6.x

The following Perl modules must be installed

    DBI
    DBD::mysql
    Bio::DB::Fasta
    Bundle::BioPerl
    Bio::Seq
    Bio::DB::Sam

If you have trouble installing the Bio::DB::Sam package, you may have to
edit the Makefile and add a -fPIC flag.

You need to have the following module installed in Python:

    virtualenv