CrossTalkZ/README at master · uzbit/CrossTalkZ · GitHub

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ABOUT

CrossTalkZ is a tool for the statistical analysis of cross-talk between groups (e.g. pathways)
as evidenced by a given network's topology. This file has information about building, using, and citing this tool.

BUILDING

The CrossTalkZ tool only requires two components of the BOOST (http://www.boost.org/) C++ library,
libxml2, a standard c++ compiler and cmake. One can obtain the source code for the boost from the
website, however most Unix based platforms have installation packages. libxml2 and cmake are already
installed on most unix systems. If you have boost (>= 1.45), libxml2 and cmake installed skip to the
next section.

LINUX INSTRUCTIONS:
Using your favorite package installation technique, search for and install
the current version of:
	libboost-graph or just boost-graph
	libboost-program_options or just boost-program_options
	libxml2 or just xml2 development version (-dev)
	cmake
Also installing any required packages.


MAC INSTRUCTIONS:
The easiest way to install boost on a mac is to use macports.
http://www.macports.org/
Once it is installed execute the following commands:
sudo port selfupdate
sudo port install boost
sudo port install libxml2
sudo port install cmake

Source instructions for boost:
If you wish to install boost from source, which should work for most platforms
an installation HOWTO can be found here:
http://ubuntuforums.org/showthread.php?t=1180792

The only thing that is ubuntu specific in that HOTO is ensuring that
the required build environment (gcc, libc, etc) is installed.

SBC MODULE:
To add the CrossTalkZ module on the sbc pdc cluster type the following commands:
export MODULEPATH=$MODULEPATH:/afs/pdc.kth.se/projects/sbc/modules/system/
module add i-compilers/11.1 openmpi
module add crosstalkz

To add the CrossTalkZ module on a personal computer following commands:
export MODULEPATH=$MODULEPATH:/afs/pdc.kth.se/projects/sbc/modules/system/
module add crosstalkz

COMPILATION

This project uses cmake to configure and generate a Makefile.
To configure cmake, edit src/CMakeLists.txt
Find set command for CMAKE_CXX_COMPILER and change to your compiler of choice. e.g. "g++" for Gcc

Then, in the CrossTalkZ root directory, you should be able to simply run the following two commands:

cmake src/
make

If errors are generated, most likely either the boost library or libxml2
were not found or are not installed properly on the system.

EXECUTION

The tool has two required parameters and some other options. To view these run the
program without any parameters.

The NETWORK_FILE is a network file that can have one of three formats:
1) XGMML file format
2) Tab separated file of the form:
PROTEIN1	PROTEIN2	[optional edge weight to compare with cutoff]
If no edge weight is provided then a link between PROTEIN1 and PROTEIN2 is in the network.
3) Unabridged tab separated FunCoup file.

The GROUPS_FILE is currently a tab separated file containing the following columns:
[] denote optional columns
GENE	GROUP	[USER_SPECIFIED]


CITATION

If you use this program for a published work please use the following citation:

McCormack T, Frings O, Alexeyenko A, Sonnhammer ELL (2013) Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks. PLoS ONE 8(1): e54945. doi:10.1371/journal.pone.0054945