Cytoscape-Sapelo2 - Revision history

Shtsai at 00:29, 5 April 2026

2026-04-05T00:29:53Z

← Older revision		Revision as of 20:29, 4 April 2026
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==
	<pre class="gcommand">		<pre class="gcommand">
	ml Cytoscape/3.9.1-Java-11		ml Cytoscape/3.9.1-Java-11

Shtsai at 00:29, 5 April 2026

2026-04-05T00:29:28Z

← Older revision		Revision as of 20:29, 4 April 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==

	3.9.1		3.9.1

	=== Author / Distributor ===		== Author / Distributor ==

	Please see https://cytoscape.org/		Please see https://cytoscape.org/

	=== Description ===		== Description ==

	"Cytoscape is an open source software tool for integrating, visualizing, and analyzing data in the context of networks."		"Cytoscape is an open source software tool for integrating, visualizing, and analyzing data in the context of networks."
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	more details at [http://www.cytoscape.org/documentation_users.html CytoScape]		more details at [http://www.cytoscape.org/documentation_users.html CytoScape]

	=== Running Program ===		== Running Program ==


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	[[#top\|Back to Top]]		[[#top\|Back to Top]]
	=== Installation ===		== Installation ==

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

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Shtsai at 19:15, 20 March 2025

2025-03-20T19:15:44Z

← Older revision		Revision as of 15:15, 20 March 2025
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	[[Category:~~Teaching~~]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		=== Category ===

Chelsea: Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === 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 [http://www.cytoscape.org/documentation_users.html CytoScape] === Running Program ===..."

2024-05-14T16:14:21Z

Created page with "Category:Teaching Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === 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 [http://www.cytoscape.org/documentation_users.html CytoScape] === Running Program ===..."

New page

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== 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 [http://www.cytoscape.org/documentation_users.html CytoScape]

=== Running Program ===

*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
<pre class="gcommand">
ml Cytoscape/3.9.1-Java-11
</pre>

This program has a graphical interface. Please refer to [[Running_Jobs_on_the teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] and [[Running_Jobs_on_the teaching_cluster#How_to_run_an_interactive_job_with_Graphical_User_Interface_capabilities | 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
<pre class="gcommand">
interact -x11
ml Cytoscape/3.9.1-Java-11
Cytoscape [options]
exit
</pre>

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):
<pre class="gscript">
#!/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]
</pre>

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:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===
<pre class="gcommand">
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.
</pre>

[[#top|Back to Top]]
=== Installation ===

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

=== System ===
64-bit Linux