Biowulf High Performance Computing at the NIH
tappas on Biowulf

From the documentation:

TappAS is a bioinformatics application containing a wide range of analyses to evaluate the functional impact of Alternative Transcript Expression Mechanisms (AltTEM), in the form of a GUI application developed in Java and R. To do this, tappAS relies on A) a series of statistical methods to evaluate different aspects of post-transcriptional processing and B) a functional annotation file containing positional information for functional motifs and domains at the transcript and CDS levels.

This is a graphical application, so a graphical connection to biowulf is required (see our docs here)

References:

  • de la Fuente, L., Arzalluz-Luque, Á., Tardáguila, M. et al. tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing. Genome Biology 2020, 21:119 Pubmed |  PMC |  Journal
Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=4 --mem=10g --gres=lscratch:20
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ export TMPDIR=/lscratch/${SLURM_JOB_ID:-none}/tmp
[user@cn3144]$ mkdir ${TMPDIR:-none}
[user@cn3144]$ module load tappas
[user@cn3144]$ cp -r ${TAPPAS_TEST_DATA:-none}/tappAS_projectData .
[user@cn3144]$ java -Xmx9g -Djava.io.tmpdir=$TMPDIR -jar $TAPPAS_JAR

It may be necessary to install some R package into your private R library

Please the the official tappas documentation and/or the tutorial for a detailed explanation of how to use the tappas GUI.

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$