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:
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