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

Mon Mar 31 14:12:50 UTC 2008

Hello

A while ago I sent a message asking for help. Someone guided me (I thank him a lot) but I am still struggling with the installation of Emboss Explorer. I have seeked for documentation but could not find any.  I am using this forum since I do not know where else to apply. I wish this is OK.

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?

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?

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?

Thank you in advance for the help. It will be appreciate very much.

Johanne Duhaime
duhaimj at ircm.qc.ca<mailto:duhaimj at ircm.qc.ca>