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Welcome to the HPC Wiki for the [http://bioinformatics.ibers.aber.ac.uk Bioinformatics] research group at [http://www.aber.ac.uk 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.
 
Welcome to the HPC Wiki for the [http://bioinformatics.ibers.aber.ac.uk Bioinformatics] research group at [http://www.aber.ac.uk 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.
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== Editing this Wiki ==
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Please email ibers-cs@aber.ac.uk to ask for access to edit this wiki.
  
 
== Troubleshooting ==
 
== Troubleshooting ==
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[[Asking for Help]]
 
[[Asking for Help]]
  
[[Minimal, Verifiable, Complete example]]
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== Remote Working Resources ==
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[[VPN and SSH via central]]
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[[Copying files with SCP/WinSCP/Filezilla/Cyberduck]]
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[[Running graphical programs remotely]]
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== Super Computing Wales Guides ==
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[[SCW Introduction]]
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[[SCW Training Materials]]
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[[SCW Access Procedures]]
  
  
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[[Module Environment]]
 
[[Module Environment]]
  
[[Submitting your job using SGE]]
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[[Installing your own modules]]
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[[Submitting your job using Slurm]]
  
 
[[Complex submissions]]
 
[[Complex submissions]]
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[[ABySS]]
 
[[ABySS]]
  
[[Updated Scheduler]]
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== Tools to access the HPC (Windows) ==
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[[Putty]]
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[[MobaXterm]]
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[[Filezilla]]
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== Slides, Talks and Training Materials==
  
[[WinSCP from external]]
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Talk on using Containers - [[File:Containers.pdf]]
  
== Slides and Talks ==
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[https://scw-aberystwyth.github.io/IBERS-HPC-tutorial/ Carpentries Style Lesson on using the HPC]
  
[[File:Sge queue changes.pdf]]
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[https://bioinformatics.ibers.aber.ac.uk/training/IBERS%20HPC%20Tutorial%20Recording.mp4 Recording of the lesson above]
  
 
== Bioinformatics Working Group related ==
 
== Bioinformatics Working Group related ==
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[[Diamond Blast]]
 
[[Diamond Blast]]
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[[Singularity Containers]]
  
 
== Other Services ==
 
== Other Services ==
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[[Genome Annotation]]
 
[[Genome Annotation]]
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== Tips ==
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[[Splitting Multifastas]]
  
 
== Workarounds ==
 
== Workarounds ==
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[[Java memory allocation issues]]
 
[[Java memory allocation issues]]
  
[[convert_fasta_to_1l_fasta.sh]]
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[[convert_fasta_to_1l_fasta.sh]]´

Latest revision as of 12:15, 19 December 2022

IBERS-logo-Bi.jpg


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.

Editing this Wiki

Please email ibers-cs@aber.ac.uk to ask for access to edit this wiki.

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

Remote Working Resources

VPN and SSH via central

Copying files with SCP/WinSCP/Filezilla/Cyberduck

Running graphical programs remotely

Super Computing Wales Guides

SCW Introduction

SCW Training Materials

SCW Access Procedures


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

Installing your own modules

Submitting your job using Slurm

Complex submissions

Monitoring your jobs

Available Software

UNIX Graphical interface

Array jobs

ABySS

Tools to access the HPC (Windows)

Putty

MobaXterm

Filezilla

Slides, Talks and Training Materials

Talk on using Containers - File:Containers.pdf

Carpentries Style Lesson on using the HPC

Recording of the lesson above

Bioinformatics Working Group related

Meeting minutes

Special HPC Workflows

Matlab

Blast

Active Perl

SPRINT

Progressive Cactus

OrthoMCL

Diamond Blast

Singularity Containers

Other Services

Blast2go

Best Practice

Running BLAST optimally

Use scratch space

Tutorials

RNA Seq on HPC

RNA Seq on HPC (using Trinity)

Genome Annotation

Tips

Splitting Multifastas

Workarounds

Java memory allocation issues

convert_fasta_to_1l_fasta.sh´