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Oakley, Ruby

Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language.

Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, integrating ordinary functions, manipulating polynomials, and integrating ordinary differential and differential-algebraic equations. It is easily extensible and customizable via user-defined functions written in Octave's own language, or using dynamically loaded modules written in C++, C, Fortran, or other languages.

While our python installations come with many popular packages installed, you may come upon a case where you need an addiditonal 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.

To be able to install a package using the conda package manager:

Oakley, Owens, Ruby

While we provide a number of Python modules, you may need a module we do not provide. If it is a commonly used module, or one that is particularly difficult to compile, you can contact OSC Help for assistance, but we have provided an example below showing how to build and install your own Python modules, and make them available inside of Python.

Oakley, Owens, Ruby

OSC provides Allinea Performance Reports and Allinea MAP to all OSC users. 

  • Allinea Performance Reports: very simple tool to generate one single-page HTML report that presents overall performance characteristics of HPC applications
  • Allinea MAP: HPC application profiler with easy-to-use GUI environment.

Versions

The following versions of Allinea are available on OSC clusters:

Oakley, Owens, Ruby

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.

Owens

Early Access Period

Owens is expected to be available to all OSC clients on a later date to be announced. A small number of projects will be given access during the preceding several weeks to help us with testing and to provide feedback. Early access is by application only; the application deadline has passed.

Early access will be granted in several stages beginning August 22, 2016. Applicants will receive notification of their access date via ServiceNow.

Oakley, Owens

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

Availability and Restrictions

The following versions of BamTools are available on OSC clusters:

Oakley, Owens

STAR: Spliced Transcripts Alignment to a Reference.

Availability and Restrictions

The following versions of STAR are available on OSC clusters:

Oakley, Owens

miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs. The tool reports known and hundreds of novel microRNAs with high accuracy in seven species representing the major animal clades. The low consumption of time and memory combined with user-friendly interactive graphic output makes miRDeep2 accessible for straightforward application in current reasearch.

Oakley, Owens

STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.

Availability and Restrictions

The following versions of STAR-Fusion are available on OSC clusters:

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