[EMBOSS] question about EMBOSS-GUI help system

[Jean Mao]

Hi,

I have installed emboss-gui from Luke McCarthy on our test server. I am trying to solve a problem and your help will be greatly appreciated. 

Problem:
I selected a program on left panel, clicked on the 'help' link on right panel, clicked the 'go' link, the detail info about that specific program will be displayed. there are 2 links in this page 'go to the input files for this example' and 'go to the output files for this example'. When I click on either link, instead of taking me to where the input/output files are at the lower part of the same page, it will take me back to the EMBOSS-GUI homepage which is the same page I click 'help' image. Since the help page is created on the run, I assume the #input and #output in the html code failed to find the tag and therefore load the base html page.

For your info, the following is the info I entered at the install.sh prompt, I also modified the file /usr/local/lib/perl5/site_perl/5.6.1/EMBOSS/GUI.pm (see below):
--------------------------------------------------------------------------------------------------------------
# bsh install.sh
Writing Makefile for EMBOSS::ACD
Manifying blib/man3/EMBOSS::ACD.3
Installing /usr/freeware/catman/p_man/man3/EMBOSS::ACD.3
Writing /usr/local/lib/perl5/site_perl/5.6.1/irix-n32/auto/EMBOSS/ACD/.packlist
Appending installation info to /usr/freeware/lib/perl5/5.6.1/irix-n32/perllocal.pod
Writing Makefile for EMBOSS::GUI
Manifying blib/man3/EMBOSS::GUI.3
Manifying blib/man3/EMBOSS::GUI.3
Installing /usr/local/lib/perl5/site_perl/5.6.1/EMBOSS/GUI.pm
Installing /usr/freeware/catman/p_man/man3/EMBOSS::GUI.3
Writing /usr/local/lib/perl5/site_perl/5.6.1/irix-n32/auto/EMBOSS/GUI/.packlist
Appending installation info to /usr/freeware/lib/perl5/5.6.1/irix-n32/perllocal.pod
        /usr/local/bin/perl postamble.pl /usr/local/bin/perl

Please answer the following questions to set up EMBOSS::GUI:

Where was EMBOSS installed?
        [ default is /usr/local ]
> /usr/localapps/emboss
Where was the EMBOSS data installed?
        [ default is /usr/localapps/emboss/share/EMBOSS ]
> 
Where were the EMBOSS binaries installed?
        [ default is /usr/localapps/emboss/bin ]
> 
Where is the root of the web server document tree?
        [ default is /home/httpd ]
> /info/www1/htdocs
Where should the EMBOSS::GUI HTML files be installed?
        [ default is /info/www1/htdocs/html/EMBOSS ]
> /info/www1/htdocs/EMBOSS-GUI
What is the hostname of the web server EMBOSS::GUI will be installed on?
        [ default is localhost ]
> nimbus.nih.gov:8888
What is the URL corresponding to the HTML directory above?
        [ default is http://nimbus.nih.gov:8888/EMBOSS ]
> http://nimbus.nih.gov:8888/EMBOSS-GUI 
Where should the EMBOSS::GUI CGI script be installed?
        [ default is /info/www1/htdocs/cgi-bin ]
> /info/www1/cgi-bin
What is the URL corresponding to the CGI directory above?
        [ default is http://nimbus.nih.gov:8888/cgi-bin ]
> 

Installing EMBOSS::GUI HTML files...

Generating default configuration files...
Finds or fetches the data files read in by the EMBOSS programs

And that should just about do it.  Point your browser at
http://nimbus.nih.gov:8888/EMBOSS-GUI/index.html to try it out...

Please report any errors or strange occurrences to lukem at bioinfo.pbi.nrc.ca
-------------------------------------------------------------------------------------------------------------

modify /usr/local/lib/perl5/site_perl/5.6.1/EMBOSS/GUI.pm:
-----------------------------------------------------------------------------------------
command out line $ENV{'PLPLOT_LIB'} = "$EMBOSS_HOME";

add 
$ENV{'PLPLOT_LIB'} = "/usr/localapps/emboss/plplot/lib";
$ENV{'EMBOSSRC'} = "/usr/localapps/emboss";

change 
$ENV{'PATH'} = "$EMBOSS_BIN:/bin";
to
$ENV{'PATH'} = "$EMBOSS_BIN:/bin /usr/local/bin";
-------------------------------------------------------------------------------------------

chmod a+r /info/www1/htdocs/EMBOSS-GUI/images/

Thank you very much.

Jean
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