From WARP3D's webpage:
WARP3D is under continuing development as a research code for the solution of large-scale, 3-Dsolid models subjected to static and dynamic loads. The capabilities of the code focus on fatigue & fracture analyses primarily in metals. WARP3D runs on laptops-to-supercomputers and can analyze models with several million nodes and elements.
The following versions of WARP3D are available on OSC clusters:
R is a language and environment for statistical computing and graphics. It is an integrated suite of software facilities for data manipulation, calculation, and graphical display. It includes
More information can be found here.
Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
While our Python installations come with many popular packages installed, you may come upon a case in which you need an additional package that is not installed. If the specific package you are looking for is available from anaconda.org (formerlly binstar.org), you can easily install it and required dependencies by using the conda package manager.
ARM HPC tools analyze how HPC software runs. It consists of three applications, ARM DDT, ARM Performance Reports and ARM MAP:
Sometimes the best way to get access to a piece of software on the HPC systems is to install it yourself as a "local install". This document will walk you through the OSC-recommended procedure for maintaining local installs in your home directory or project space. The majority of this document describes the process of "manually" building and installing your software. We also show a partially automated approach through the use of a bash script in the Install Script section near the end.
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
The following versions of BamTools are available on OSC clusters:
STAR: Spliced Transcripts Alignment to a Reference.
The following versions of STAR are available on OSC clusters:
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
The following versions of Trimmomatic are available on OSC clusters:
