Resources and Assignments:
2. Lecture 2: Introduction to UNIX Pt. 1
As a reference we summarized the more frequently used commands on a UNIX system in an online table.
3. Install Cygwin / XFree UNIX environment
You can test the tools introduced in Lecture 2 with the free cygwin UNIX implementation for Windows. Later, you can use cygwin to perform many tasks on your Windows laptop that would normally require a UNIX computer. At the same time, you can access the files directly from within Windows, creating a powerful mixed OS environment without the need to connect to a remote Linux computer with SSH.
Click on this link and download the file "cygwin_xfree_setup.exe" to your laptop. Start the executable. Right-mouse click once on the circular sign next to "All". Leave window alone for a few minutes, don't click on anything else. When function changes from "Default" to "Install" click "Next". Select a nearby download site, e.g. the NASA FTP site is reasonably fast. For more info on cygwin see the extensive online documentation. We are not going to use X-free X-Window System in the first session, but you can read more about it here.
There are two widely used UNIX text editors (Lecture 2), emacs and vi. Emacs is more powerful and more user-friendly, but only vi can be run directly in a terminal window such as provided by an SSH client. To take advantage of emacs editing capabilities on your Windows system, you can now install the Windows version of the program.
Click on this link and
download the file "emacs-21.3-fullbin-i386.tar.gz" to your laptop.
Place the file in your cygwin home directory (you may have to start
cygwin first from the Start menu to create your home directory). Then
extract the files from the tarball using the following command:
tar xvfz emacs-21.3-fullbin-i386.tar.gz
Then move the entire extracted directory "emacs-21.3" to a
desired location on your laptop (e.g. to "Program Files") and delete
the tarball. You can create a shortcut under Windows to the emacs
executable "runemacs.exe" (in bin) and place this shortcut to your
Windows Programs menu or to your desktop. For more info on emacs see
the extensive GNU online
documentation.
You can log into your student account and transfer files to and from the account using the programs ssh and sftp from within cygwin. However, cygwin sftp file transfer does not provide a graphical window or point and click convenience. Also, the cygwin shell does not allow copy-and-paste from outside the shell window under Windows.
Therefore, we recommend
that you install the SSH Communications SSH client, which is free for
academic, non-commerical use. Click on this link and
download the file "SSHSecureShellClient-3.2.5.exe" to your laptop. Then
install and configure the software. For more info on this SSH client
use the Help menu. Note: When connecting to the host machines, if the
machine name (DNS entries) are not found, try the numeric IP addresses
(see Lecture 2).
Note: the two login
machines mentioned in class should not be used for running jobs. More
info on that later.
6. Preparations for Next Class
Please bring your laptop
and have the following installed/downloaded:
(repeat from last week):
Please read the handouts on
proteins and nucleic acids, in addition to the
reading suggested in the last session. The author of these handouts is
P. G. Debrunner, UIUC, 1993.