CoNet - Command line
This page contains a script and a manual for running CoNet on command line (with bash).
The CoNet package up to version 1.1.1.beta contains an old command line script that is
outdated by now and the script shared here is recommended instead.
The script uses the data of tutorial 5 as an example.
To run it, place the script in a folder with two sub-folders named Input and Output and copy
the two input files (the count data and the pH values)
from tutorial 5 into the Input folder. After having set the path to the CoNet jar file, you
can then launch the script in bash with command ./. As explained in the header
of the script, you have to launch it repeatedly to perform the different steps (threshold computation,
permutations, bootstraps and final network construction). Please also make sure that you have the permission
to read the files in the input folder, write into the output folder and to execute the script.
In bash, permissions can be changed with chmod.
The script can be run locally or on a cluster. Several jobs can be
run in parallel to compute permutations and bootstraps, also when run locally.
Concerning the cluster management software, the script has been tested for Torque and Sungrid Engine,
but it is easy to adapt it to other management systems.
You can load the final network in gdl format into Cytoscape using the CoNet plugin. For this, open the "Network loading"
menu (lower left corner of the main menu), select the network file and click GO.
For more instructions on command line, please read this manual.
