Stat/Biostat 550: 2014: statgen.stat.washington.edu

Getting Started: two options.:

• 1. The Statistics department has set up a virtual linux computer statgen.stat.washington.edu, and installed the software needed for this class. All participating students (and others) for whom I have provided the UW NetIDs to Statistics should be able to access, using their UW NetID. For security, it may have been set up so we could access only via an on-campus system, but if so I will get that changed . For those used to linux operating systems (or who want to learn to use linux) this may be the easiest way to do things.
• 2. For those using Windows, or Mac OSX 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; I cannot provide help with any Windows software issues.

1. For those following option (1), please check you can follow the instructions below. If you do not plan to use the Statistics computer statgen.stat.washington.edu for your class computing, you do not need to do this..

2. For those following option (2) it may be useful to 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. The actual software here is istalled on the Biostatistics computing system, and most will not be used in this class. However, the links will be useful for those downloading their own copies of software.

Accessing and using statgen.stat.washington.edu:

1. A useful document of basic linux commands is at Useful Unix Commands. Only a very few of these will be needed.

2. Log in to the computer named statgen.stat.washington.edu. using an SSH program. If you are starting out on a Linux computer (for example, one of the department or UW Linux servers), you can ssh into other computers by typing:

   % ssh name@statgen.stat.washington.edu

   where name is your UW NetID.
   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.

3. 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@statgen.stat.washington.edu

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

4. 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, see Introduction to Linux at Biostat. Even though this refs to the Biostat computers, it was updated in 2012, and should work equally well for statgen.stat.washington.edu. Since I do not use Windows, I probably cannot provide much more help, but if having difficulties, please let me know.
   
   
5. Now you are almost ready to start: Log in to statgen.stat.washington.edu if not alread logged in.
   
   
6. To check you can access software type

% which PHASE


The machine should with respond with "/usr/local/bin/PHASE". It is telling you which PHASE command it will use for you: PHASE is the program we will use in the first lab.
If the machine responds with "PHASE: Command not found", something is not done right.
Try again, and/or let me know. As a last resort, contact the Statistics computing staff, (help@stat.washington.edu).


7. 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

Of course, you can make directories of different names for the different labs, and or a hierarchy of subdirectories. Or you can just put everything in one directory, even your home directory.

For more information on these commands, or on using a Linux or UNIX system in general,
see http://depts.washington.edu/statgen/Computing/linux-tut.html
(Note this is writen for the (now long gone) Biostat computer aleph, but the commands do not change,