.. _test_pipeline_run:

Test Grape with a predefined minimal test dataset
=================================================

Before using the Grape buildout, you need to have access to a MySQL database.

Put the MySQL database connection information into your home folder::

    $ vim ~/.my.cnf

This is the example configuration that you can adapt to your system. Change the
host to your MySQL host::

    [client]
    host=localhost
    user=rnaguest
    password=rnaguest

Ask your database administrator for a login of the rnaguest user and read/write
access to the following two databases on this host:

* Test_RNAseqPipeline

* Test_RNAseqPipelineCommon

Check out the buildout from svn::

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

Edit the dependencies.cfg file to point to the location of the Java and Perl 
binaries::

    [settings]
    java = /soft/bin/java
    perl = /soft/bin/perl

Get the testdata::

    $ wget -m 'ftp://ftp.encode.crg.cat/pub/rnaseq/pipeline/testdata' --directory-prefix=src/testdata --no-directories

Create a virtual environment and run the buildout::

    $ /path/to/your/python/bin/virtualenv --no-site-packages .
    $ ./bin/python ../../bootstrap.py
    $ ./bin/buildout

After running buildout, the parts folder contains the fully configured RNASeq
pipeline inside the TestRun folder::

    [+] parts
        [+] TestRun

Go the TestRun RNASeq pipeline and start it::
 
    $ cd parts/TestRun
    $ ./start.sh

Then execute the pipeline::

    $ ./execute.sh