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Welcome to the HPC Wiki for the Bioinformatics research group at Aberystwyth University. The aim of this wiki is to allow researchers in the field of Bioinformatics in IBERS at Aberystwyth to document common tasks using the High Performance Computing cluster.

Contents

Troubleshooting

Please read these sections if you are having trouble. There is a chance that you can resolve the problem on your own and ask for help more effectively otherwise. Some (most) of these ideas are shamelessly taken from the stackoverflow help pages.

Asking for Help

Minimal, Verifiable, Complete example


IBERS HPC Guides

Overview

Bert and Ernie - An Overview

Nodes, Cores, Slots

Scheduling and queuing

Getting an account

Using the HPC

Quick start

Your disk space

Module Environment

Submitting your job using SGE

Complex submissions

Monitoring your jobs

Available Software

UNIX Graphical interface

Array jobs

ABySS

Updated Scheduler

WinSCP from external

Slides and Talks

File:Sge queue changes.pdf

Bioinformatics Working Group related

Meeting minutes

Special HPC Workflows

Matlab

Blast

Active Perl

SPRINT

Progressive Cactus

OrthoMCL

Diamond Blast

Other Services

Blast2go

Best Practice

Running BLAST optimally

Use scratch space

Tutorials

RNA Seq on HPC

RNA Seq on HPC (using Trinity)

Genome Annotation

Workarounds

Java memory allocation issues

convert_fasta_to_1l_fasta.sh