[EMBOSS] EmbossExplorer: running problem (or installation problem?)

Thu Apr 10 12:27:02 EDT 2008

> Here is my first question.
> 
> "index.html" file in my Emboss web directory contains the following:
> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN"
>  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd">
> <html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en' lang='en'>
>   <head>
>     <title>EMBOSS Explorer</title>
>   </head>
>   <frameset cols="170, *">
>     <frame src="/cgi-bin/emboss/menu" name="menu" />
>     <frame src="/cgi-bin/emboss/intro" name="main" />
>   </frameset>
> </html>
> in my "cgi-bin" I only have "emboss" as a perl program after the installation. How could that work?

The main page (index.html) directs your browser to use two frames.  Both 
frames are generates by the /cgi-bin/emboss script.  The script 
recognizes the URL as either /menu or /intro and displays the pages 
accordingly.  The script uses the ACD files installed by EMBOSS to 
determine what application are available, their groups, etc.

> Of course if I rename emboss by, let's say intro (as in the index.html), it does work. But I have three frames.  What am I missing?

You shouldn't rename the script.  If you do, it can break the whole 
package.  I don't know why you would have three frames. What browser are 
you using?  Here is a proper installation, http://emboss.umdnj.edu

Did the additional frame appear after you renamed the script?

> My second question
> I want to change the default output for "emma". For this I have put "SET emboss_OUTFORMAT clustal"  in my "emboss.default" file. This work perfectly when I use "emma" at the command line. But it has no effect in the EmbossExplorer Interface. Is there a way to correct that?

The web server doesn't see that environment variable hence it never gets 
passed to emma.  You can either set the environment variable in a 
startup script for your web server, or (the more proper way is to) 
modify your emma.acd file to include that output format as an option. 
(Please refer to the appropriate documentation on how to accomplish 
either method)

Ryan