Available Software

There is a lot of software available on the IBERS HPC machine. If something is not available, please contact your systems administrator.

Some of these programs are available as a module so will require loading, while others are installed by default.

To see available modules, type;

 module avail

into the command line, and this will show you what is available. See the page about the Module Environment for details about loading and unloading modules.

Software available on Bert - The login node

This software is available for use on the login node (bert), which means you can work on this machine and then once the workflow has been created, you can submit the workflow to Sun Grid Engine (SGE) for processing.

File Editing Software

Since you will be accessing the HPC machine via the command line, you do not usually have access to a graphical interface. Therefore a command line editor is very useful. You can use this to write software, edit workflows or even write documents.

nano - A very simple lightweight file editor. Very simple to use. [1]

vi - A standard UNIX editor available on most systems. This is quite complex to use, but once mastered it is very useful. [2]

X11 Software

X11 is a UNIX Graphical User Interface (GUI). Since Bert and Ernie have no monitors attached to it, much of the work you will be doing will be from the command line. However, X11 in UNIX allows you to stream the user interface over the network so that you can view certain programs on your local screen. Here are a few of these applications;

evince - PDF viewer. This allows you to view pdf files stored on the HPC on your local machine without downloading the pdf file to your local machine.

eog - Eye Of GNOME - a simple lightweight image viewer to view image files (BMP, JPEG, PNG, TIFF, GIF, PNM, RAS, ICO, XPM, SVG)

gedit - A simple text editor that is useful for highlighting code or making documents/work flows directly on the HPC

Software available natively on Nodes

gnuplot - Very simple to use and can produce fantastic plots in various file formats. [3]

pth-devel 2.0.7-9.3 was installed across the nodes

SCons v2.0.1.r5134 installed across the nodes

Software Installed as Modules

ActivePerl/5.14.2

ncbi-blast-2.2.28+ (when loading BLAST/2.2.28 it loads blast+ 2.2.28 but legacy blast 2.2.26. This will be updated soon)

bcl2fastq/1.8.3

GNU Parallel 20131022

clustalw2/2.1

stacks/1.08

Matlab - this is quite restrictive at the moment, only on the large node (large.q) as we don't have floating licences for this at the moment and the queue management software does not deal with multiple users, therefore you job will fail if another user runs a matlab job at the same time. This is still work in progress as we don't have many users for this. For more info on this see http://bioinformatics.ibers.aber.ac.uk/wiki/index.php/Matlab

R

 R/3.0.2 - with bioclite, rlecuyer,boot,e1071 and sprint 1.0.4 - NOTE: the version of R with FIEmspro is still installed on version 2.14.2

casava/1.8.2

 R/R-2.14.2

BLAST: Basic Local Alignment Search Tool - Finds regions of local similarity between sequences

 BLAST/blast-2.2.26
 BLAST/blast-2.2.28

Active Perl

Casava

R - R is a free software environment for statistical computing and graphics

perl/5.18.1

Java - 1.7.0_03

gcc (C/C++ and F95) - 4.4.6

repeatmasker/R-2.14.2

trinity/2013-02-25

usearch/6.0.307

Weka/Weka-3.6.6