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<DIV><STRONG><FONT size=2>Hi,</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV>
<DIV><FONT size=2><STRONG>I have installed emboss-gui</STRONG> <STRONG>from Luke
McCarthy on</STRONG> <STRONG>our test server. I am trying to solve a problem and
your help will be greatly appreciated.</STRONG> </FONT></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><STRONG><FONT size=2>Problem:</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>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.</FONT></STRONG></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><STRONG><FONT size=2>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):</FONT></STRONG></DIV>
<DIV><STRONG><FONT
size=2>--------------------------------------------------------------------------------------------------------------<BR>#
bsh install.sh</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>Writing Makefile for EMBOSS::ACD<BR>Manifying
blib/man3/EMBOSS::ACD.3<BR>Installing
/usr/freeware/catman/p_man/man3/EMBOSS::ACD.3<BR>Writing
/usr/local/lib/perl5/site_perl/5.6.1/irix-n32/auto/EMBOSS/ACD/.packlist<BR>Appending
installation info to
/usr/freeware/lib/perl5/5.6.1/irix-n32/perllocal.pod<BR>Writing Makefile for
EMBOSS::GUI<BR>Manifying blib/man3/EMBOSS::GUI.3<BR>Manifying
blib/man3/EMBOSS::GUI.3<BR>Installing
/usr/local/lib/perl5/site_perl/5.6.1/EMBOSS/GUI.pm<BR>Installing
/usr/freeware/catman/p_man/man3/EMBOSS::GUI.3<BR>Writing
/usr/local/lib/perl5/site_perl/5.6.1/irix-n32/auto/EMBOSS/GUI/.packlist<BR>Appending
installation info to
/usr/freeware/lib/perl5/5.6.1/irix-n32/perllocal.pod<BR>
/usr/local/bin/perl postamble.pl /usr/local/bin/perl</FONT></STRONG></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><STRONG><FONT size=2>Please answer the following questions to set up
EMBOSS::GUI:</FONT></STRONG></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><STRONG><FONT size=2>Where was EMBOSS
installed?<BR> [ default is /usr/local
]<BR>> /usr/localapps/emboss<BR>Where was the EMBOSS data
installed?<BR> [ default is
/usr/localapps/emboss/share/EMBOSS ]<BR>> <BR>Where were the EMBOSS binaries
installed?<BR> [ default is
/usr/localapps/emboss/bin ]<BR>> <BR>Where is the root of the web server
document tree?<BR> [ default is
/home/httpd ]<BR>> /info/www1/htdocs<BR>Where should the EMBOSS::GUI HTML
files be installed?<BR> [ default is
/info/www1/htdocs/html/EMBOSS ]<BR>> /info/www1/htdocs/EMBOSS-GUI<BR>What is
the hostname of the web server EMBOSS::GUI will be installed
on?<BR> [ default is localhost
]<BR>> nimbus.nih.gov:8888<BR>What is the URL corresponding to the HTML
directory above?<BR> [ default is
</FONT></STRONG><A href="http://nimbus.nih.gov:8888/EMBOSS"><STRONG><FONT
size=2>http://nimbus.nih.gov:8888/EMBOSS</FONT></STRONG></A><STRONG><FONT
size=2> ]<BR>> </FONT></STRONG><A
href="http://nimbus.nih.gov:8888/EMBOSS-GUI"><STRONG><FONT
size=2>http://nimbus.nih.gov:8888/EMBOSS-GUI</FONT></STRONG></A><STRONG><FONT
size=2> <BR>Where should the EMBOSS::GUI CGI script be
installed?<BR> [ default is
/info/www1/htdocs/cgi-bin ]<BR>> /info/www1/cgi-bin<BR>What is the URL
corresponding to the CGI directory
above?<BR> [ default is
</FONT></STRONG><A href="http://nimbus.nih.gov:8888/cgi-bin"><STRONG><FONT
size=2>http://nimbus.nih.gov:8888/cgi-bin</FONT></STRONG></A><STRONG><FONT
size=2> ]<BR>> </FONT></STRONG></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><STRONG><FONT size=2>Installing EMBOSS::GUI HTML
files...</FONT></STRONG></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><STRONG><FONT size=2>Generating default configuration files...<BR>Finds or
fetches the data files read in by the EMBOSS programs</FONT></STRONG></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><STRONG><FONT size=2>And that should just about do it. Point your
browser at<BR></FONT></STRONG><A
href="http://nimbus.nih.gov:8888/EMBOSS-GUI/index.html"><STRONG><FONT
size=2>http://nimbus.nih.gov:8888/EMBOSS-GUI/index.html</FONT></STRONG></A><STRONG><FONT
size=2> to try it out...</FONT></STRONG></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><STRONG><FONT size=2>Please report any errors or strange occurrences to
</FONT></STRONG><A href="mailto:lukem@bioinfo.pbi.nrc.ca"><STRONG><FONT
size=2>lukem@bioinfo.pbi.nrc.ca</FONT></STRONG></A></DIV>
<DIV><STRONG><FONT
size=2>-------------------------------------------------------------------------------------------------------------</FONT></STRONG></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV>
<DIV><STRONG><FONT size=2>modify
/usr/local/lib/perl5/site_perl/5.6.1/EMBOSS/GUI.pm:</FONT></STRONG></DIV>
<DIV><STRONG><FONT
size=2>-----------------------------------------------------------------------------------------</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>command out line $ENV{'PLPLOT_LIB'} =
"$EMBOSS_HOME";</FONT></STRONG></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><STRONG><FONT size=2>add </FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>$ENV{'PLPLOT_LIB'} =
"/usr/localapps/emboss/plplot/lib";<BR>$ENV{'EMBOSSRC'} =
"/usr/localapps/emboss";</FONT></STRONG></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV>
<DIV><STRONG><FONT size=2>change </FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>$ENV{'PATH'} =
"$EMBOSS_BIN:/bin";</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>to</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2>$ENV{'PATH'} = "$EMBOSS_BIN:/bin
/usr/local/bin";</FONT></STRONG></DIV>
<DIV><STRONG><FONT
size=2>-------------------------------------------------------------------------------------------</FONT></STRONG></DIV>
<DIV><FONT size=2></FONT> </DIV>
<DIV><STRONG><FONT size=2>chmod a+r
/info/www1/htdocs/EMBOSS-GUI/images/</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV>
<DIV><STRONG><FONT size=2>Thank you very much.</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=2></FONT></STRONG> </DIV>
<DIV><STRONG><FONT size=2>Jean</FONT></STRONG></DIV></DIV></DIV></BODY></HTML>