Requirements
Minimum Requirements
If you only want to store your Sircah-generated data in an XML file, you will need:
- Python 2.4 or higher.
- The elementtree package for Python.
- If you would like to use the coverage level visualisation you will also need the Python matplotlib package.
Relational Database Setup
If you would like to use Sircah with a relational database you will need to install:
- The SQLAlchemy package, version 4.
the database software:
- SQLite version 3 or higher.
- MySQL version 4 or higher.
- PostgreSQL. Sircah has been tested with version 8.2.
and corresponding database API:
Installation
Download Sircah-1.0.tar.gz and unpack:
~/downloads/>tar -zxf Sircah-1.0.tar.gz ~/downloads/>cd Sircah-1.0
To carry out a standard installation:
~/downloads/>python setup.py build ~/downloads/>python setup.py install
This will place the Sircah executable scripts (sircah_detect.py, sircah_add_alignments_to_genes.py, sircah_visualise.py) in the same directory as the python executable, if you would to specify an alternative directory you can do so with the --install-scripts option:
~/downloads/>python setup.py build ~/downloads/>python setup.py install --install-scripts ~/scripts
