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

Thu Apr 10 13:19:24 EDT 2008

Thank so much for your answers. Regarding the first one, I really appreciate.
As you can see in my email, the index.html was set as in the example you proposed me.
Then saying:
"The main page (index.html) directs your browser to use two frames.  Both
frames are generates by the /cgi-bin/emboss script."
Just wakes me up.
My installation was /cgi-bin/emboss/emboss!!!
So in my index.html I changed:
"/cgi-bin/emboss/menu" for "/cgi-bin/emboss/emboss/menu"

Such a lost of time for such trivial thing...

Thanks again

Johanne
-----Message d'origine-----
De : Ryan Golhar [mailto:golharam at umdnj.edu]
Envoyé : Thursday, 10 April 2008 12:27
À : Duhaime Johanne
Cc : 'emboss at emboss.open-bio.org'
Objet : Re: [EMBOSS] EmbossExplorer: running problem (or installation problem?)

> 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