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 (formerly binstar.org), you can easily install it and required dependencies by using the conda package manager.
Linaro HPC tools analyze how HPC software runs. It consists of three applications, Linaro DDT, Linaro Performance Reports and Linaro 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 OSC provides a template Install Script to automate building and installing your software. There is also a description here of how to "manually" build and install your software.
STAR: Spliced Transcripts Alignment to a Reference.
The following versions of STAR are available on OSC clusters:
SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).
The following versions of SnpEff are available on OSC clusters:
The Sequence Read Archive (SRA Toolkit) stores raw sequence data from "next-generation" sequencing technologies including 454, IonTorrent, Illumina, SOLiD, Helicos and Complete Genomics. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. Use SRA Toolkit tools to directly operate on SRA runs.
The following versions of SRA Toolkit are available on OSC clusters:
Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc.
The following versions of Ncview are available on OSC clusters:
The Subread package comprises a suite of software programs for processing next-gen sequencing read data like Subread, Subjunc, featureCounts, and exactSNP.
The following versions of Subread are available on OSC clusters:
VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
The following versions of VCFtools are available on OSC clusters:
