Oakley

Octave

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.

Allinea

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:

All ACLs lost in Home Directories after 6/7 downtime

Date: 
Tuesday, June 7, 2016 - 6:00pm
Supercomputer: 

All ACLs set within the Home Directory filesystem (/nfs/##) were lost during the 6/7 downtime.  This was caused by the migration to a new server that does not support the old POSIX ACLs.

Migrating the ACLs was not possible due to both the fact POSIX ACLs are not easily translatable to NFSv4 ACLs, and none of our tools supported such a migration.

BamTools

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:

STAR

STAR: Spliced Transcripts Alignment to a Reference.

Availability and Restrictions

The following versions of STAR are available on OSC clusters:

miRDeep2

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.

Availability and Restrictions

The following versions of miRDeep2 are available on OSC clusters:

STAR-Fusion

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:

HOMER

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.

Availability and Restrictions

The following versions of HOMER are available on OSC clusters:

MIRA

MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.

Availability and Restrictions

The following versions of MIRA are available on OSC clusters:

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