Stat/Biostat 550 2012 Computing information

Getting Started:

You do not need to do anything on this page unless you plan to use the Biostatistics Computers for your Class computing. For those used to linux operating systems (or who want to learn to use linux) this may be the easiest way to do things.
For those using Windows, or MAC you may prefer to download your own copies of software. I will provide links where you can do this. I will also make data files for labs available on the web.
Please note however that I am NOT a Windows user.

This information is modified from the lab information first developed by Amy Anderson, 2001. This version is updated from 2006, but not everything regarding Biostat computing may be current, particularly with the March 2012 move to the Tower. Kirk did update this page in 2012.

For linux information provided by the Biostat department see: UNIX Boot Camp 2010 and Useful Unix Commands. Note that these materials also refer to abacus -- remember to use hercules.

There are are a few things you should do before you begin the Labs for Stat550, or other StatGen computing.

  1. You will need to have a Biostat account. This account gives you access to the machines that contain the programs we will be using this quarter. I have provided a list of UW NetIDs to the Biostat Computing Systems person. He should send you information (password etc.) about your account.
  1. Make sure you can access the StatGen computing web pages. These web pages are maintained on the central UW system and are password-protected. That is, you will need to use your UWNet ID to access them.

Once you have a biostat account, you can proceed to step three:

 

  1. Log in to the computer named hercules.biostat.washington.edu. using an SSH program. If you are starting out on a Linux computer (for example, one of the Statistics department Linux servers), you can ssh into the Biostat machines by typing:

    % ssh name@hercules.biostat.washington.edu

    where name is your user name for your biostat account (don’t actually type the % sign—it’s just there to denote the prompt that should already be sitting on your screen). Your prompt sign may be a ``$'' sign instead of a %, or something else.

    If logging in from a Unix/Linux system, you may like to get into the habit of using the -X option on ssh:

    % ssh -X name@hercules.biostat.washington.edu

    That way, if you ever want to use X-windows graphics (for example for Pedfiddler) it might work.

    From a Windows PC, you can use the SSH Tectia Client that comes as part of the UWICK software set. If you need more detailed information on logging in, take the link on the StatGen computing web pages that says Introduction to Linux at Biostat (or this link here!).

    Since I do not use Windows, I probably cannot provide much more help, but if having difficulties, please let me know.

  1. It is recommended that students use hercules rather than abacus or markov which are being retired. Software for all the labs is being reinstalled using hercules.

Now you are almost ready to start:


  1. To be able to use the StatGen programs, you need to fix up your .cshrc file to include the line

    2. source ~statgen/.statgen.cshrc

    You can do this using this command:

    echo "source ~statgen/.statgen.cshrc" >> .cshrc


  1. For step 5 to take effect, you will either need to log out and log in again, or else type the exact same line as you put into your .cshrc file at the command prompt. To check it has worked, type

% which pedcheck

The machine should with respond with "/home/guests/statgen/x86_64-linux/bin/pedcheck". It is telling you which pedcheck command it will use for you: pedcheck is a program we will use in the first lab.
If the machine responds with "pedcheck: Command not found", something is not done right.
Try again, and/or let me know. As a last resort, contact the Biostat computing staff, (bite@u.washington.edu).
If it responds with a different pedcheck (for example /usr/local/bin/pedcheck or .../i386-linux/bin/pedcheck), then please let me know -- I have been having trouble getting the new software paths set correctly.


  1. One last set-up thing that is not essential, but which you probably will find useful. Make a special directory in which to keep all your StatGen files this quarter. To make a new directory entitled “My550”, just type

% mkdir My550

Then, to get into your new directory, type

% cd My550

For more information on these commands, or on using a Linux or UNIX system in general, take the link UNIX/Linux tutorial from the Introduction to Biostat Computing page. The web page you are going to has the address: http://depts.washington.edu/statgen/Computing/linux-tut.html
Again, Kirk Le updated that page in 2012.