Cytoscape-Teaching
Category
Bioinformatics
Program On
Teaching
Version
3.7.2
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 Sapelo2
- Version 3.7.2 is installed in /usr/local/apps/eb/Cytoscape/3.7.2
To use version 3.7.2, please first load the module with
module load Cytoscape/3.7.2
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
xqlogin module load Cytoscape/3.7.2 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 module load Cytoscape/3.7.2 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
module load Cytoscape/3.7.2 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.
Installation
Code downloaded from https://cytoscape.org/download-platforms.html
System
64-bit Linux