Using X windows on barra or hebrides

WIBR Bioinformatics and Research Computing

Using X windows on barra or hebrides

To use X Windows on barra on hebrides, Mac users can choose between X11 (a free product) or eXodus. PC users can choose between Cygwin/X or VNC, both of them free.

Installing Cygwin/X

Cygwin/X is Cygwin, a Linux-like environment for Windows, together with X windows functionality. Cygwin adds the functionality of many Unix/Linux tools. to your Windows computer through a command-line interface. Cygwin/X adds the graphical interface.
If you don't have Cygwin, install Cygwin with X-windows support.
If you already have Cygwin but may need to add X-windows support, go through the Cygwin set-up procedure again and add the packages openssh (the OpenSSH server and client programs) and xorg-x11-base (Cygwin/X Base), as described in install Cygwin with X-windows support.

Connecting the first time with VNC:

If needed, download the Free Edition VNC for Windows or another OS (choosing the "viewer program only") to anywhere on your desktop computer.
Use the secure shell to connect to barra as usual. If you've never done this before, download SSHWinClient from SSH (for Windows). The file will look like SSHSecureShellClient-?.?.?.exe
After logging in to barra, issue the following command: vncserver
Since this is the first time for running this command, you will be asked to select a password (that can be changed later with this command: vncpasswd). This password need not be (but can be) the same as your barra login password.
A second time, issue the following command: vncserver

Read the message you get back; it should be something like

	New 'X' desktop is barra:18

	Creating default startup script /home/your_user_name/.vnc/xstartup
	Starting applications specified in /home/your_user_name/.vnc/xstartup
	Log file is /home/your_user_name/.vnc/barra:18.log

Go to wherever you put the viewer application on your desktop and click to run it.
When the window pops up, type in
```
barra.wi.mit.edu:n
```
where "n" is number you received after running 'vncserver' (18 in the example above)
After entering the appropriate number, i.e.,

click "OK" and enter the password you just chose.
The X windows screen should pop up on your desktop ==> you're ready to go.
See below for some applications that take advantage of the graphical interface
Closing your desktop window doesn't terminate the session. Just reconnect by clicking on the viewer on your desktop and entering the session details.
To permanently end this session, enter the command
```
vncserver -kill :n
```
(where "n" is the number of the session [18 in the above example])
If you forget your VNC password, use the command
```
vncpasswd
```
to reset it.

Connecting subsequent times with VNC:

Use the secure shell to connect to barra as usual.
After logging in to barra, issue the following command: vncserver

Read the message you get back; it should be something like

	New 'X' desktop is barra:18

	Creating default startup script /home/your_user_name/.vnc/xstartup
	Starting applications specified in /home/your_user_name/.vnc/xstartup
	Log file is /home/your_user_name/.vnc/barra:18.log

Go to wherever you put the viewer application on your desktop and click to run it.
When the window pops up, type in
```
barra.wi.mit.edu:n
```
where "n" is number you received after running 'vncserver' (18 in the example above)
After entering the appropriate number, i.e.,

click "OK" and enter your x windows password.
The X windows screen should pop up on your desktop ==> you're ready to go.
See below for some applications that take advantage of the graphical interface
Closing your desktop window doesn't terminate the session. Just reconnect by clicking on the viewer on your desktop and entering the session details.
To permanently end the session, enter the command
```
vncserver -kill :n 
```
(where "n" is the number of the session [18 in the above example])

Connecting on a Mac with X11:

Using X11 requires newer versions of Mac OS X (10.3 and later)

If needed, download and install X11 from Apple (download page)
Open X11 (Applications > Utilities > X11).
For connecting, go to 'xterm' and enter ssh -X -l username barra.wi.mit.edu,
where username is the name of your barra account.
Note: Using the above command without the '-X' allows text transmission but no graphics.
For file transfer, sftp username@barra.wi.mit.edu,
where username is the name of your barra account.

Connecting on a Mac with eXodus:

If needed, download the MacSSH_PPC folder from the Applications volume of Enigma.
Run eXodus (double-click on the icon) but do NOT use it to open a session.
Run the ssh application (in the folder you downloaded from Enigma) and use it to login to barra using your username and password.
In the ssh window, find out the hostname of the machine you are connecting to barra from by running the command 'who' and locating your username and current session in the list.
In the ssh window, type the command:
```
setenv DISPLAY hostname.wi.mit.edu:0
```
replacing 'hostname' with the hostname you found from the 'who' command
To move files between the Macintosh and barra - from the Macintosh select AppleShare and the Ethernet zone. Then choose barra from the Select a file server box. Type in your barra login name and password and click okay. Your barra volume is now mounted.

Some applications:

To get a menu with many of these applications customized for barra and hebrides, place the file twmrc into your home directory and rename it to .twmrc The next time you start X windows, it'll take effect.

command	application
xterm	classic command window
xemacs	xemacs (popular text editor)
xemacs -bg black -fg white	open xemacs with custom colors
nedit	open nedit (easy-to-use text editor)
clustalx	perform a multiple alignment (help)
jalview seqFile FASTA	edit a multiple alignment (help)
matlab	Matlab package (help)
phoenix	Mozilla web browser
setenv DISPLAY unix:foo.0	set display if needed
who -m	get name of display
xclipboard	Clipboard (to help with copying and pasting)
clock	an analog clock
xclock -d	a digital clock
xcalc	calculator
xload	see how hard barra is working
xman	unix (man) help pages
echo $DISPLAY	Get your display for this session

Help:

Your mouse must be over a window to use the keyboard in that window.

Use the upper right hand icon in most windows to resize them. They must be made larger before they can be made smaller.

If you forget your VNC password (or want to change it), go to the Unix prompt, type 'vncpasswd', and enter a new password.

To close a window with no pull-down menu, click with BOTH mouse buttons at the same time anywhere but on a window, and the cursor should turn into a skull-and-crossbones. Then place the cursor over the window to close, and use the left mouse button. If you don't get the skull-and-crossbones cursor, you may have to modify the configuration of your desktop VNC viewer. To do so, close your VNC desktop and go through the steps to re-open it, but before entering the connection information, click on "Options...", click on the "Inputs" tab, and check the box next to "Enable 3-button mouse emulation". Then click on the "Defaults" tab and click on "Save As Defaults". Reconnect as you did the first time, and now you should have the skull-and-crossbones functionality.

If you placed the .twmrc file in your home directory, click on the background with the left mouse button to get a menu of some applications. Note that "Applications" leads to GCG, Matlab, and SAS. Clicking on the background with the right mouse button opens another menu. One of the choices, "Show Iconmgr", may be helpful to stay organized if lots of windows are open at once.

If copying and pasting doesn't seem to work, use the clipboard (command: xlipboard &)

Going from X windows to desktop:
- Select text to be copied using the left mouse button and use 'copy' from the pull-down menu.
- Copied text should appear on the clipboard.
- Select text from clipboard and hit ENTER.
- Paste text into your desktop application.
Going from desktop to X windows:
- Select and copy text as usual.
- While mouse is on a new clipboard, hit both mouse buttons at once.
- Paste text into X windows application.

Problem: For some applications, you may receive an error message such as

	Xlib: Client is not authorized to connect to Server

	SeqLab cannot open your display.
	Please do a setenv DISPLAY ... and try again.
	Make sure your display authorizes connections from your host.
	Consult your system manager for help.

Solution: issue the command

	setenv DISPLAY unix:n.0

where "n" is the number for your specific connection (18 in the example above).

For thorough help about connecting, see the online documentation for Virtual Network Computing