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 provides a variety of ways to get software.
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.
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.
SDS is yet another ITS initiative to provide low cost software. Their website is the best place to get more information.
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.
Members of the Gutell Lab can get copies of Microsoft software downloaded from the lab's Microsoft Developer's Network account.
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.
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.
BioPython - Installed on clusters. Use /opt/rocks/bin/python as your python interpreter.
Consed/Phred/Phrap
IDEA - Interactive Display for Evolutionary Analyses Installed on genomes in /share/apps/idea.
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