https://github.com/fenderglass/Ragout
Revision ac511e2bd23f9c54a5c77ecd59ee08386e744811 authored by kolmogorov on 09 March 2014, 17:15:41 UTC, committed by kolmogorov on 09 March 2014, 17:15:41 UTC
1 parent c300ebd
Tip revision: ac511e2bd23f9c54a5c77ecd59ee08386e744811 authored by kolmogorov on 09 March 2014, 17:15:41 UTC
small fix for cactus
small fix for cactus
Tip revision: ac511e2
INSTALL.md
Installation instructions for Ragout
====================================
Ragout is written in Python and does not require any preparations.
However, there are some third-party dependencies described below
which need to be installed.
Quick dependencies
------------------
* python 2.7
* biopython [http://biopython.org]
* networkx [http://networkx.github.io]
* Sibelia [https://github.com/bioinf/Sibelia]
Python
------
Ragout is written in python and requires version 2.7 to run.
Also, there are third-party dependencies:
* biopython [http://biopython.org]
* networkx [http://networkx.github.io]
You can install them with your OS-specific package manager,
e.g. in Ubuntu:
$ sudo apt-get install python-biopython python-networkx
or using pip package manager:
$ pip install biopython networkx
If you use Python 2.5 or 2.6, you need to install additional Python
packages:
* argparse [https://pypi.python.org/pypi/argparse]
Sibelia
-------
Ragout uses *Sibelia* for decomposing genomes into synteny blocks.
You may install it by running:
$ python bin/install-deps.py
Building process requires *Cmake* as well as some standard UNIX
executables like *wget* or *tar*.
Computing file changes ...