First, all access to UT systems is subject to the UT Acceptable Use Policies . You should read these, and make sure you understand what your rights and responsibilities are. You should also read our Information Security Audit page to see more information about computers audits we are required to perform. If you will be bringing your own computer, or laptop into the PAT 141 office we would appreciate knowing about it, so that we can get the info we need for the audit.
Next, join the mailing list for the system(s) you are going to be using. Lists are maintained on the UTLISTS system. To join a list, click on one of the links below. You'll be taken to the UTLISTS system and asked to provide your email address. If you have done this before, you'll be asked for the password, and then you will be added to the list. If you have not joined a list yet, a new account will be created, and you will be sent a password to confirm that you have given a valid email address. Then you will be added to the list. Note, that these lists are moderated, so don't panic if your (un)subscribe attempts are not immediately accepted. Posts to the lists will also have to be approved.
- Phylo Cluster Discussion and Announcement List
- Jansen Lab Genomes Server
- Hofmann Lab's Cichlid Server
- Wilke Lab Cluster
- CCBB mailinglist
- CCBB collaborators
While you are messing around with your email client you should add our trouble email: remark at ccbb.utexas.edu. Note that this is not gripe@ like many other computer groups on campus use, because we do not consider asking for help and complaining to be the same thing. Remember that if you do not tell us about a problem, or issue we cannot address it. Also, we are not mind readers, so please provide as much information as possible.
Next you should log in and set up your email forwarding as described on our Email page. More information about our systems is on our hardware page.
You can review the software we have available.
To use the cluster/UNIX systems effectively you may want to get some software. First of all if you want to edit UNIX files on your PC or Mac, then you should download an appropriate editor. This is discussed further on our file server page specifically in the section Ascii vs Binary section. To log in, you need to get a Secure Shell Client. Some options are discussed on the Secure Shell page. Some people also use a Virtual Network Computing client for this, but we do not currently support this. You might want a secure file transfer program, as discussed on the file server page . Finally, if you are going to be running any GUI programs on the cluster you'll want some X-server software for your PC or Mac (Linux users will have this by virtue of logging in on the desktop). For Mac users, you can use the Apple provided software which you might have to download, or get off the installation media. PC users have a number of choices. Xming , and Cygwin are two free choices.
Our clusters are Linux based, so to get the maximum use of them you'll need to become familiar with the UNIX command line, which is a powerful text based interface which lets you type in commands to the computer for evaluation. This can be a bit of a barrier to getting your work done, but with perseverance you can learn enough UNIX to be at least able to use the cluster. While we can answer some quick, "how do I do this", or "why is this" type questions, in the long term it's better that you bite the bullet and get this done. Here are some resources that we have run across
- O'Reilly and Assocates publishes very good books that range from beginner to reference. In particular, Learning the UNIX Operating System is very good.
- Computer Science offers CS 108: UNIX, 1 hour course that is meant for beginners. If you don't take the class you might sit in, or get the book Linux: The Textbook which is pricey, but also very good.
- Several people have taken courses offered by Perl Source Informatics but they can be pricey.
You may also find loads of stuff using Google, and hopefully we will write our own version. It's just the case that right now we need more work on infrastructure, so spending time writing up own on version of things is counterproductive. If someone is willing to buy some of these reference texts, and donate them to use, we are willing to serve as the library. We will also be willing to track interest in the Perl Source Informatics courses as they do have bulk purchasing prices.
Initially when you use the cluster you can use some of our pre-canned scripts. After awhile you will probably be interested in write your own, or perhaps you will be forced to do so. While you can continue to use our scripts as templates for your own you might also want to get some books on scripting, and programming. First, you can get quite decent scripting done just by learning more about the shell we use which is the BASH shell. O'Reilly and Associates ahs a book on BASH which is called Learning the BASH Shell . This would also be useful for people wanting just to learn more about the powerful things they can do on the command line, or who want more information about the things they can do to customize their environment. They also have books on Perl, and Python for people interested in using BioPerl, or BioPtyhon. Computer Science also has Perl, Python, C++, and possibly other programming classes listed under the CS 105 class heading http://x.cygwin.com/. You will also want to read our documentation on the SGE Batch system which you will use to submit jobs to the cluster.
