HOWTO: Add python packages using the conda package manager

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:

HOWTO: Install your own python modules

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. Note, these instructions use "bash" shell syntax; this is our default shell, but if you are using something else (csh, tcsh, etc), some of the syntax may be different.


Allinea software analyzes how HPC software runs. It consists of two applications, Allinea Performance Reports and Allinea MAP: 

All ACLs lost in Home Directories after 6/7 downtime

Tuesday, June 7, 2016 - 6:00pm

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 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: Spliced Transcripts Alignment to a Reference.

Availability and Restrictions


The following versions of STAR are available on OSC clusters:


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 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 (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:


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