Cytoscape-Teaching: Difference between revisions
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(Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 3.7.2 === Author / D...") |
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=== Version === | === Version === | ||
3. | 3.9.1 | ||
=== Author / Distributor === | === Author / Distributor === | ||
| Line 23: | Line 23: | ||
=== Running Program === | === 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 | |||
*Version 3. | |||
To use version 3. | To use version 3.9.1, please first load the module with | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ml Cytoscape/3.9.1-Java-11 | |||
</pre> | </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]]. | |||
This program has a graphical interface. Please refer to [[ | |||
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 | 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"> | <pre class="gcommand"> | ||
interact -x11 | |||
ml Cytoscape/3.9.1-Java-11 | |||
Cytoscape [options] | |||
exit | exit | ||
</pre> | </pre> | ||
| Line 55: | Line 47: | ||
Example of a job submission script sub.sh to run a batch job (note: this is not the cytoscape execution command script): | 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"> | <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] | cytoscape.sh [options] | ||
</pre> | </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. | 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: | Example of submission to the queue: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
sbatch ./sub.sh | |||
</pre> | </pre> | ||
=== Documentation === | === Documentation === | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ml Cytoscape/3.9.1-Java-11 | |||
cytoscape.sh -h | cytoscape.sh -h | ||
| Line 92: | Line 89: | ||
format). | format). | ||
-S,--script <file> Execute commands from script file. | -S,--script <file> Execute commands from script file. | ||
-R,--rest <port> Start a rest service. | -R,--rest <port> Start a rest service. | ||
</pre> | </pre> | ||
Latest revision as of 14:19, 6 September 2023
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.
Installation
Code downloaded from https://cytoscape.org/download-platforms.html
System
64-bit Linux