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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. | ||
| − | + | == 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 [https://stackoverflow.com/help/ 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]] | [[Bert and Ernie - An Overview]] | ||
| + | |||
| + | [[Nodes, Cores, Slots]] | ||
| + | |||
| + | [[Scheduling and queuing]] | ||
| + | |||
| + | [[Getting an account]] | ||
| + | |||
| + | '''Using the HPC''' | ||
[[Quick start]] | [[Quick start]] | ||
| + | |||
| + | [[Your disk space]] | ||
[[Module Environment]] | [[Module Environment]] | ||
| − | [[Submitting your job using | + | [[Installing your own modules]] |
| + | |||
| + | [[Submitting your job using Slurm]] | ||
[[Complex submissions]] | [[Complex submissions]] | ||
| Line 23: | Line 63: | ||
[[UNIX Graphical interface]] | [[UNIX Graphical interface]] | ||
| − | == Special Workflows == | + | [[Array jobs]] |
| + | |||
| + | [[ABySS]] | ||
| + | |||
| + | == Tools to access the HPC (Windows) == | ||
| + | |||
| + | [[Putty]] | ||
| + | |||
| + | [[MobaXterm]] | ||
| + | |||
| + | [[Filezilla]] | ||
| + | |||
| + | == Slides, Talks and Training Materials== | ||
| + | |||
| + | Talk on using Containers - [[File:Containers.pdf]] | ||
| + | |||
| + | [https://scw-aberystwyth.github.io/IBERS-HPC-tutorial/ Carpentries Style Lesson on using the HPC] | ||
| + | |||
| + | [https://bioinformatics.ibers.aber.ac.uk/training/IBERS%20HPC%20Tutorial%20Recording.mp4 Recording of the lesson above] | ||
| + | |||
| + | == Bioinformatics Working Group related == | ||
| + | |||
| + | [[Meeting minutes]] | ||
| + | |||
| + | == Special HPC Workflows == | ||
[[Matlab]] | [[Matlab]] | ||
| + | |||
| + | [[Blast]] | ||
| + | |||
| + | [[Active Perl]] | ||
| + | |||
| + | [[SPRINT]] | ||
| + | |||
| + | [[Progressive Cactus]] | ||
| + | |||
| + | [[OrthoMCL]] | ||
| + | |||
| + | [[Diamond Blast]] | ||
| + | |||
| + | [[Singularity Containers]] | ||
| + | |||
| + | == Other Services == | ||
[[Blast2go]] | [[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]]´ | ||
Latest revision as of 12:15, 19 December 2022
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
- 1 Editing this Wiki
- 2 Troubleshooting
- 3 Remote Working Resources
- 4 Super Computing Wales Guides
- 5 IBERS HPC Guides
- 6 Tools to access the HPC (Windows)
- 7 Slides, Talks and Training Materials
- 8 Bioinformatics Working Group related
- 9 Special HPC Workflows
- 10 Other Services
- 11 Best Practice
- 12 Tutorials
- 13 Tips
- 14 Workarounds
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.
Remote Working Resources
Copying files with SCP/WinSCP/Filezilla/Cyberduck
Running graphical programs remotely
Super Computing Wales Guides
IBERS HPC Guides
Overview
Using the HPC
Submitting your job using Slurm
Tools to access the HPC (Windows)
Slides, Talks and Training Materials
Talk on using Containers - File:Containers.pdf
Carpentries Style Lesson on using the HPC
Special HPC Workflows
Other Services
Best Practice
Tutorials
RNA Seq on HPC (using Trinity)
