Acquiring Software

The following are some resources regarding purchasing software. You might also want to look down below at what we have already installed. If you don't find the software you are looking for, please ask us about it. It might be that we do have it and it's just not listed anywhere below, or it might be that we can obtain it for you, possibly in concert with others to get bulk discounted or site licensing so that we all benefit.

UT Provided

UT provides a variety of ways to get software.

BevoWare

Bevoware is a collection of useful utility type software. At the very least you should visit this site and grab a copy of the Virus software which is required on all computers on the UT network. Other software to be found here includes personal firewalls, spy ware detectors, web browsers, FTP and SSH clients, and Acrobat Reader.

Campus Computer Store

In addition to offering computer Hardware, the Campus Computer Store is the provider for Microsoft Campus Select Agreement items. The MCSA program is an agreement for UT to provide students, staff, and faculty with common and useful utilities, such as Operating Systems, Office, and Visual Studio, at greatly reduced costs. The Campus Computer Store additionally offers a selection of other commericial software often with Academic or Educational prices.

If you interested in buying a MCSA product for a UT owned system, please see us. In this case, UT has negotiated access to volume licensed CDs, and we might already have one that you can use for your install.

The Campus Computer Store is located in Flawn Academic Center. They also have a webpage.

Software Distribution and Sales

SDS is yet another ITS initiative to provide low cost software. Their website is the best place to get more information.

UT FTP Website

ITS' Telecommuncations & Networking Department maintains a server which mirrors very many Open Source projects. Despite being named, ftp.utexas.edu, software may be downloaded using ftp, http, or rsync. Best of all downloads from ftp.utexas.edu do not count against your off-campus bandwidth quota.

MSDN

Members of the Gutell Lab can get copies of Microsoft software downloaded from the lab's Microsoft Developer's Network account.

Natural Science Licensed

The College of Natural Sciences has licensed Mathematica and Labview. To download these visit the Physics IT Group's webpage.

When downloading Mathematica, faculty and staff have a few options. First, if you are installing Mathematica onto a system that will always be at UT, then download the site and networked license version. We have a license server which you can use, and this may make it easier to keep updated, as we will take steps to keep the license updated. Please contact us for more information about using the server. If you wish to run Mathematica on a UT owned laptop, then download the non-conforming version. Finally, faculty and staff can download the Home Use version for computers that they have at home, and then following the instructions on the download page to get a license from Wolfram.

If you need help downloading and installing this software, please let us know.

NOTE: The current version of Mathematica is 7. Physics is currently evaluating the licensing and other details of Mathematica 8, and then they will provide that version instead.

Software Installed on CCBB Systems

General Notes

Generally Linux, and Solaris systems will have add-on software installed in /share/apps. This is because the clusters install extras this way, and it seems wise to keep things consistent. Some things may also be installed in /usr/local/bin, or /usr/bin, if they were obtained prepackaged and this is where the package puts them. However, for consistency I am trying to avoid prepackaged software.

NOTE: The clusters, and UNIX systems are slowly moving over to use the Modules infrastructure. This will make it easier to use the software packages below; however, you should read our tutorial on using the modules

Since we do not know what people are using, the question as to whether a particular version is installed depends entirely on us being asked to upgrade, so if you think something should be updated. Likewise, we make our best effort to install any requested software. When asking for a 3rd party package to be installed it's useful if you send along a link to its home page. Some things in the list below may not be available due to some licensing issue; however, we mention them in order that we can track usage to determine when there is enough interest to either purchase it, or begin coordinating the purchase by interested parties.

Some packages may allow additional modules to be installed (notably perl, python, and R). When we upgrade a version of one of these packages, we commit to only upgrading that package and a set of core modules discussed in the section for that package. For example, with python we commit to upgrading Numpy, Scipy, and BioPython with each upgrade. If you want other modules installed after an upgrade you will need to request it after each upgrade. If enough people ask that a module be regularly installed, if enough people ask for it after an upgrade, or if a given lab mentions that they consistently need a particular module for their support we will added it to the supported list. This policy is implemented not to cause problems, or delays in processing but simply because it takes a certain bit of work to upgrade some of these tools, and some of this work can be avoided by not continuing to install packages that were originally installed only because someone wanted to test something out. Note that these same packages also let you keep you own local module repository, and you are welcome (or maybe even encouraged) to do so while testing, or long term. Avoid trying to do too much installing, especially when you are trying to testing something out. We can usually install much faster once we know something is needed.

General purpose tools

• ATLAS is a programming library which aims to provide very fast linear algebra routines.
  Installed on phylocluster in /share/apps/atlas. On other clusters/systems may be installed in /usr/lib and /usr/include.h as part of the atlas-3.6.0 package.
• Blast
• BEAST 1.8.0 was installed in phylocluster
• Bioconductor
• Bioperl

• BioPython - Installed on clusters. Use /opt/rocks/bin/python as your python interpreter.

• BioMart Perl APIs
• NCBI Eutils
• Qiime 1.7.0 is installed on phylocluster.
• R
• Python
• Mathematica (installed in /share/apps/bin/math on phylocluster. Also installed is mash.pl a program which can be used to run .m files on the nodes. See http://ai.eecs.umich.edu/people/dreeves/mash/] for more details.)
  
• Mat-lab -UT has site-licensed Mat lab 2013.
• LAPACK is a set of libraries which allow common linear algebra procedures to be performed. LAPACK depends on BLAS for much of the low-level calculations.
• BLAS libraries are hardware tuned routines to work on matrices. Likely you would use this not by itself, but as part of ATLAS or LAPACK.
  
• Graphics programs
• BOOST libraries
• Phred, Phrap, Consed, cross_match, daev
• Picard
• Hmmer
• Data compression programs
• Clustering programs - MCL and usearch, uclust
• ssh - generating keys

Microarray data analysis tools

• MeV

NGS Data Quality Control Tools

• Fastx Toolkit
• FastQC
• Get FASTQ Format

Mappers/Aligners

• mapreads SOLiD data only, ungapped alignment
• MAQ - best for short-read SNP calling; ungapped alignment
• muscle - "old school" aligner - good for 454 amplicons
• SOAP - very fast and versatile: any read length, gapped, paired-end, SNP calling
• SSAHA & SSAHA2 - like Maq, fast for ungapped mapping - SNP calling, contig placement to reference, etc.
• Bowtie - very fast, ungapped alignment. Does not support color space data
• SHRiMP - A sensitive and accurate mapper. Supports color space data and gapped alignment.
• BFAST - BLAT-like short read mapper. Natively supports SOLiD colorspace short reads.
• BWA - The successor to MAQ; a BW mapper, but which allows for gaps and handles colorspace natively.
• GMAP and GSNAP - Mappers for cDNA and very sensitive detection of short indels.
• Mosaik - A suite of alignment and reference-guided assembly tools.
• See Category:Mapper for more details.

Gene prediction tools

• GeneWise
• Geneid
• glimmer3

SNP discovery and Annotation

• Corona-Lite - SOLiD data only
• Breakdancer
• Genome Analysis Tool Kit (GATK)
• MAQ - best for short-read SNP calling; ungapped alignment
• Picard
• SOAP - very versatile: any read length, gapped, paired-end, SNP calling
• SAMTOOLS
• Annovar

RNA-Seq Analysis

• Tophat-Cufflinks-Cuffdiff, ignoring novel transcripts
• Tophat-Cufflinks-Cuffdiff, allowing for novel transcripts
• Removing duplicates from alignment output

Splice Junction discovery

• Tophat- Cufflinks

Genome Alignment and Visualization

• Circos
• IGV
• MaqView
• Mauve
• Affymetrix Integrated Genome Browser: easy to install genome browser. Download here
• SAMStat

De novo assembly

• MIRA
• Velvet
• ABYSS
• Using consed, including editing Mira assemblies
• ABI's SOLiD de novo pipeline
• Phred, Phrap, Consed, cross_match, daev
• Allpaths-LG
• Mosaik - A suite of alignment and reference-guided assembly tools.
• (Newbler, the Roche/454 assembler, is under 454 Analysis tools)

Transcriptome de novo assembly

• Trinity
• SOAPtrans

ABI pipelines

• Small RNA Pipeline

454 Analysis tools
Current Roche/454 software versions on Fourierseq are all 2.5.3. Tarballs of various 454 software versions are available at /home/daras/454sw*

• Sff file manipulation tools - Utilities to convert and manipulate 454 sff files.
• GS De novo assembler - Performs assembly of reads and generates contigs.
• GS Reference mapper - Maps reads to a reference genome and reports consensus and variants.
• GS Amplicon variant analyzer - For detection of variants in amplicon libraries : a small region of interest at very large coverage.
• GS Run processor and run browser - Generally run already by the GSAF, but you might want to re-process image data sometimes.
• Georgiou Lab Amplicon scripts - Matlab scripts...
• BLAST tools(NCBI BLAST and WU-BLAST) - Scripts for quick and dirty blasts of 454 reads and contigs to see what's going on at a global level

Other software

• MeV

• Consed/Phred/Phrap

• IDEA - Interactive Display for Evolutionary Analyses Installed on genomes in /share/apps/idea.

• IM/IMa

• Intel Compiler Suite

• Mr. Bayes

• PAML Installed on genomes in /share/apps/paml/bin. Documentation is in /share/apps/paml/docs, and examples in /share/apps/paml/examples.

• Paup is currently disabled while we determine its licensing status. If you would like to be consulted when/if we decide to purchase it, please let us know.

• PLINK  is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

• Phylip Installed on genomes in /share/apps/phylip. Documentation is in /share/apps/phylip/docs.

• RAxML is installed on phylocluster in /share/apps/RAxML/bin. Sample datasets are in /share/apps/RAxML/samples. The http://icwww.epfl.ch/~stamatak/index-Dateien/countManual7.0.4.php manual can be downloaded from http://icwww.epfl.ch/~stamatak/index-Dateien/countManual7.0.4.php here

• Rosetta

• SATe is installed on the clusters. To use it use this job script . Here are some instructions for doing this.

• SEALS

• tRNAscan