Hi all,
I have questions regarding emboss explorer installation. Attached is the
explorer configuration file
I have emboss4.0 running in my linux machine: /usr/local/bin and
/var/www/emboss
After following instructions on the emboss explorer installation I
cannot see the webpage:
Not Found
The requested URL /cgi-bin/emboss/intro was not found on this server.
Not Found
The requested URL /cgi-bin/emboss/menu was not found on this server
Here are some directory structures:
drwxrwxr-x 2 mukatira mukatira 4096 2006-09-15 14:02 cgi-bin
drwxr-xr-x 6 mukatira mukatira 4096 2006-09-18 13:58 emboss
drwxrwxr-x 3 mukatira mukatira 4096 2006-09-15 14:02 html
-rw-r--r-- 1 mukatira mukatira 1457 2006-09-11 14:28 index.html
$>:/var/www$ pwd
/var/www
Under cgi-bin I do not see a folder 'emboss'
$>/var/www/cgi-bin$ ls -l
-rwxrwxr-x 1 root root 110 2006-09-18 14:34 emboss
$>:/var/www/cgi-bin$ more emboss
#!/usr/bin/perl
use strict;
use warnings;
use EMBOSS::GUI;
my $emboss = EMBOSS::GUI->new();
$emboss->go();
Thanks in anticipation.
Also, what is the best way to completely uninstall emboss.
./install
installing EMBOSS Explorer perl modules...
Writing Makefile for EMBOSS::GUI
Manifying blib/man3/EMBOSS::GUI.3pm
Manifying blib/man3/EMBOSS::ACD.3pm
Manifying blib/man3/EMBOSS::GUI::Conf.3pm
Manifying blib/man3/EMBOSS::GUI::XHTML.3pm
Installing /usr/local/share/perl/5.8.7/EMBOSS/GUI/Conf.pm
Writing /usr/local/lib/perl/5.8.7/auto/EMBOSS/GUI/.packlist
Appending installation info to /usr/local/lib/perl/5.8.7/perllocal.pod
installing EMBOSS Explorer GUI components...
I need to collect some information in order to install EMBOSS Explorer:
Where was EMBOSS installed?
(default is /usr/local)
/usr/local/bin
Where should the EMBOSS Explorer HTML files be installed?
(default is /var/www/html/emboss)
What is the URL prefix corresponding to the HTML directory above?
(default is /emboss)
Where should the EMBOSS Explorer CGI script be installed?
(default is /var/www/cgi-bin/emboss)
What is the complete URL corresponding to the CGI script
'/var/www/cgi-bin/emboss'?
(default is /cgi-bin/emboss)
installing HTML files to /var/www/html/emboss...
creating HTML index file at /var/www/html/emboss/index.html...
creating output directory at /var/www/html/emboss/output...
installing CGI script to /var/www/cgi-bin/emboss...
copying manual support files to /var/www/html/emboss/manual...
find: /usr/local/bin/share/EMBOSS/doc/programs: No such file or directory
fixing permissions...
EMBOSS Explorer is installed. Visit /cgi-bin/emboss to test it out.
Site configuration (including a list of applications to be excluded from
public access) is stored in the EMBOSS::GUI::Conf module (located at
/usr/local/share/perl/5.8.7/EMBOSS/GUI/Conf.pm).
The main style sheet, which can be edited to customize the appearance of
EMBOSS Explorer is /var/www/html/emboss/style/emboss.css. If you prefer the
look and
feel of the old EMBOSS GUI, you can use /var/www/html/emboss/style/classic.css
instead (the style sheet is specified in the EMBOSS::GUI::Conf module).
EMBOSS Explorer generates temporary output files every time an application is
used. Depending on the tasks being performed, these output files can consume
space fairly quickly. The old output can be cleaned up on a regular basis by
adding a task to the root user's crontab. The following example runs every
morning at 0400 and removes all output files that have not been accessed in
the last 24 hours:
0 4 * * * find /var/www/html/emboss/output -type d -mindepth 1 -maxdepth 1
-atime 1 -exec rm -rf {} \;
Please report any errors or strange occurrences using the bug tracker at
http://sourceforge.net/tracker/?func=add&group_id=124389&atid=699414_______________________________________________
EMBOSS mailing list
[email protected]
http://lists.open-bio.org/mailman/listinfo/emboss
