IGV-Teaching: Difference between revisions
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To run | To run IGV GUI, please follow steps as below: | ||
1. log on to Teching cluster login node using ssh with X-forwarding being turned on: | 1. log on to Teching cluster login node using ssh with X-forwarding being turned on: | ||
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Please refer to [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] for more details. | |||
Here is an example of a shell script, sub.sh, to run on the batch queue: | Here is an example of a shell script, sub.sh, to run on the batch queue: | ||
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sbatch ./sub.sh | sbatch ./sub.sh | ||
</pre> | </pre> | ||
=== Documentation === | |||
more details at [http://www.broadinstitute.org/software/igv/ IGV] | |||
=== Installation === | |||
source code from [http://www.broadinstitute.org/software/igv/ IGV] | |||
=== System === | |||
64-bit Linux | |||
Revision as of 09:54, 7 February 2019
Category
Bioinformatics
Program On
Teaching
Version
2.4.4
Author / Distributor
To cite your use of IGV in your publication:
James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. Nature Biotechnology 29, 24–26 (2011), or
Helga Thorvaldsdottir, James T. Robinson, Jill P. Mesirov. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Briefings in Bioinformatics 2012.
Description
"The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations." more details at IGV
Running Program
Also refer to Running Jobs on Sapelo2
- Version 2.4.4, installed in /usr/local/apps/eb/IGV/2.4.4-Java-1.8.0_144
To use this version of IGV, please first load the module with
module load IGV/2.4.4-Java-1.8.0_144
To run IGV GUI, please follow steps as below:
1. log on to Teching cluster login node using ssh with X-forwarding being turned on:
ssh -X MyID@teach.gacrc.uga.edu
2. Once you log on, load TASSEL and run with its GUI forwarded to your local machine:
module load IGV/2.4.4-Java-1.8.0_144 sh /usr/local/apps/eb/IGV/2.4.4-Java-1.8.0_144/igv.sh
3. When you finished, please log out with:
exit
Please refer to Run X window Jobs for more details.
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_Artemis
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=Artemis.%j.out
#SBATCH --error=Artemis.%j.err
cd $SLURM_SUBMIT_DIR
ml Artemis/17.0.1-Java-1.8.0_144
act [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
more details at IGV
Installation
source code from IGV
System
64-bit Linux