Cytoscape-Teaching

Category

Bioinformatics

Program On

Teaching

Version

3.9.1

Author / Distributor

Please see https://cytoscape.org/

Description

"Cytoscape is an open source software tool for integrating, visualizing, and analyzing data in the context of networks."

more details at CytoScape

Running Program

Also refer to Running Jobs on the teaching cluster

• Version 3.9.1 is installed in /apps/eb/Cytoscape/3.9.1-Java-11

To use version 3.9.1, please first load the module with

ml Cytoscape/3.9.1-Java-11

This program has a graphical interface. Please refer to Run interactive Jobs and Run X window Jobs.

To run this program in an interactive session using the graphical front end: Start an X terminal (Mac), X window (Windows) at the local computer first, then

interact -x11
ml Cytoscape/3.9.1-Java-11
Cytoscape [options]
exit

To run as a batch job, you might have to create a script file with the cytoscape execution commands.

Example of a job submission script sub.sh to run a batch job (note: this is not the cytoscape execution command script):

#!/bin/bash
#SBATCH --job-name=jobname
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=4gb
#SBATCH --time=04:00:00
#SBATCH --output=%j.out
#SBATCH --error=%j.err

cd $SLURM_SUBMIT_DIR

ml Cytoscape/3.9.1-Java-11

cytoscape.sh [options]

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, and the job name need to be modified appropriately as well.

Example of submission to the queue:

sbatch ./sub.sh

Documentation

ml Cytoscape/3.9.1-Java-11
cytoscape.sh -h

Cytoscape Command-line Arguments
================================
usage: cytoscape.{sh|bat} [OPTIONS]
 -h,--help             Print this message.
 -v,--version          Print the version number.
 -s,--session <file>   Load a cytoscape session (.cys) file.
 -N,--network <file>   Load a network file (any format).
 -P,--props <file>     Load cytoscape properties file (Java properties
                       format) or individual property: -P name=value.
 -V,--vizmap <file>    Load vizmap properties file (Cytoscape VizMap
                       format).
 -S,--script <file>    Execute commands from script file.
 -R,--rest <port>      Start a rest service. 

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Installation

Code downloaded from https://cytoscape.org/download-platforms.html

System

64-bit Linux