[Gmod-gbrowse] missing CGI-BIN folder

Discussion:

Gonzalo Sepulveda

2014-04-04 19:49:29 UTC

Hi! i'm writting for some help about how to proper launch GBrowse2, locally.
I followed the tutorial for installing and everything went ok, i got every
pre-requisite.
Then, i followed /var/www/gbrowse2/tutorial/tutorial.html to try one of the
example databases but couldn't get to that...

i got stucked where it says to point the browser to
localhost/cgi-bin/gb2/gbrowse/volvox

Apache2 is running Ok, i think. Here's tails of error.log

AH00558: apache2: Could not reliably determine the server's fully qualified

domain name, using 127.0.1.1. Set the 'ServerName' directive globally to
suppress this message
Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming normal
operations
Command line: '/usr/sbin/apache2'
Graceful restart requested, doing restart
AH00558: apache2: Could not reliably determine the server's fully
qualified domain name, using 127.0.1.1. Set the 'ServerName' directive
globally to suppress this message
Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming normal
operations
Command line: '/usr/sbin/apache2'
caught SIGTERM, shutting down
[Fri Apr 04 15:53:00.207955 2014] [mpm_prefork:notice] [pid 24416]
AH00163: Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming
normal operations
Command line: '/usr/sbin/apache2'

i also tried re-installing Gbrowse2 and changing the route for CGI-BIN
scripts to /var/www, still nothing.

any help will be very appreciated
Regards

Scott Cain

2014-04-04 20:24:01 UTC

Permalink

Hi Gonzalo,

The snippet of error log that you sent doesn't have anything to do with
GBrowse; it's just the normal messages one sees when apache is stopped and
started. What happens when you go to http://localhost/gbrowse2? What
about http://localhost/cgi-bin/gb2/gbrowse/yeast/? What do you see in the
browser, and what do you see in the error log?

By the way, changing the installed path of the cgi files to somewhere in
/var/www won't work unless you also modify the apache config, which would
be a pain to do. Instead, just make sure the scripts go into
/usr/lib/cgi-bin/gb2.

Scott

Post by Gonzalo Sepulveda
Hi! i'm writting for some help about how to proper launch GBrowse2, locally.
I followed the tutorial for installing and everything went ok, i got
every pre-requisite.
Then, i followed /var/www/gbrowse2/tutorial/tutorial.html to try one of
the example databases but couldn't get to that...
i got stucked where it says to point the browser to
localhost/cgi-bin/gb2/gbrowse/volvox
Apache2 is running Ok, i think. Here's tails of error.log
AH00558: apache2: Could not reliably determine the server's fully

qualified domain name, using 127.0.1.1. Set the 'ServerName' directive
globally to suppress this message
[Fri Apr 04 15:21:00.840630 2014] [mpm_prefork:notice] [pid 7004]
AH00163: Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming
normal operations
Command line: '/usr/sbin/apache2'
[Fri Apr 04 15:30:40.723617 2014] [mpm_prefork:notice] [pid 7004]
AH00171: Graceful restart requested, doing restart
AH00558: apache2: Could not reliably determine the server's fully
qualified domain name, using 127.0.1.1. Set the 'ServerName' directive
globally to suppress this message
[Fri Apr 04 15:30:40.745626 2014] [mpm_prefork:notice] [pid 7004]
AH00163: Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming
normal operations
Command line: '/usr/sbin/apache2'
[Fri Apr 04 15:52:59.138698 2014] [mpm_prefork:notice] [pid 7004]
AH00169: caught SIGTERM, shutting down
[Fri Apr 04 15:53:00.207955 2014] [mpm_prefork:notice] [pid 24416]
AH00163: Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming
normal operations
Command line: '/usr/sbin/apache2'

i also tried re-installing Gbrowse2 and changing the route for CGI-BIN
scripts to /var/www, still nothing.
any help will be very appreciated
Regards
------------------------------------------------------------------------------
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Scott Cain

2014-04-07 13:12:04 UTC

Permalink

Hi Gonzalo,

Please keep the gbrowse mailing list cc'ed.

What is in your apache error log that mentions gbrowse (if there is a 404 message, there should be something in the error log).

Scott

Sent from my iPad

Thanks Scott!
when i go to localhost/gbrowse2 i got the html about the "Generic Genome Browser, v2", the tutorials, and everything else.
the problem comes in http://localhost/cgi-bin/gb2/gbrowse/yeast/, there i got 404 =/
i also checked /usr/lib/cgi-bin/gb2 and all seems to be fine there.
Still nothing, any ideas?
Regards.

Post by Scott Cain
Hi Gonzalo,
The snippet of error log that you sent doesn't have anything to do with GBrowse; it's just the normal messages one sees when apache is stopped and started. What happens when you go to http://localhost/gbrowse2? What about http://localhost/cgi-bin/gb2/gbrowse/yeast/? What do you see in the browser, and what do you see in the error log?
By the way, changing the installed path of the cgi files to somewhere in /var/www won't work unless you also modify the apache config, which would be a pain to do. Instead, just make sure the scripts go into /usr/lib/cgi-bin/gb2.
Scott

Post by Gonzalo Sepulveda
Hi! i'm writting for some help about how to proper launch GBrowse2, locally.
I followed the tutorial for installing and everything went ok, i got every pre-requisite.
Then, i followed /var/www/gbrowse2/tutorial/tutorial.html to try one of the example databases but couldn't get to that...
i got stucked where it says to point the browser to localhost/cgi-bin/gb2/gbrowse/volvox
Apache2 is running Ok, i think. Here's tails of error.log

AH00558: apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1. Set the 'ServerName' directive globally to suppress this message
[Fri Apr 04 15:21:00.840630 2014] [mpm_prefork:notice] [pid 7004] AH00163: Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming normal operations
[Fri Apr 04 15:21:00.840641 2014] [core:notice] [pid 7004] AH00094: Command line: '/usr/sbin/apache2'
[Fri Apr 04 15:30:40.723617 2014] [mpm_prefork:notice] [pid 7004] AH00171: Graceful restart requested, doing restart
AH00558: apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1. Set the 'ServerName' directive globally to suppress this message
[Fri Apr 04 15:30:40.745626 2014] [mpm_prefork:notice] [pid 7004] AH00163: Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming normal operations
[Fri Apr 04 15:30:40.745637 2014] [core:notice] [pid 7004] AH00094: Command line: '/usr/sbin/apache2'
[Fri Apr 04 15:52:59.138698 2014] [mpm_prefork:notice] [pid 7004] AH00169: caught SIGTERM, shutting down
[Fri Apr 04 15:53:00.207955 2014] [mpm_prefork:notice] [pid 24416] AH00163: Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming normal operations
[Fri Apr 04 15:53:00.207992 2014] [core:notice] [pid 24416] AH00094: Command line: '/usr/sbin/apache2'

i also tried re-installing Gbrowse2 and changing the route for CGI-BIN scripts to /var/www, still nothing.
any help will be very appreciated
Regards
------------------------------------------------------------------------------
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Scott Cain

2014-04-07 13:45:45 UTC

Permalink

Hmm, perhaps there is more than one error log; some time apache is configured to produce error logs in different ways (though it's really difficult for me to guess how that's setup for you). Again, if Apache is giving the browser a 404 message, it should be logging that somewhere.

Scott

Sent from my iPad

Ok, i'm sorry, now cc'ed
Same as before, nothing about GBrowse in the error log tail
Gonzalo.

Post by Gonzalo Sepulveda
Hi! i'm writting for some help about how to proper launch GBrowse2, locally.
I followed the tutorial for installing and everything went ok, i got every pre-requisite.
Then, i followed /var/www/gbrowse2/tutorial/tutorial.html to try one of the example databases but couldn't get to that...
i got stucked where it says to point the browser to localhost/cgi-bin/gb2/gbrowse/volvox
Apache2 is running Ok, i think. Here's tails of error.log

i also tried re-installing Gbrowse2 and changing the route for CGI-BIN scripts to /var/www, still nothing.
any help will be very appreciated
Regards
------------------------------------------------------------------------------
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Gonzalo Sepulveda

2014-04-07 15:01:22 UTC

Permalink

couldn't find any othe error.log
but i didn't notice this error while building demo:

AH00534: apache2: Configuration error: No MPM loaded.
Apache failed to start. Perhaps the demo is already running?

i checked wich mpm is installed with /usr/sbin/apache2 -l , so:

Compiled in modules:
core.c
mod_so.c
mod_watchdog.c
http_core.c
mod_log_config.c
mod_logio.c
mod_version.c
mod_unixd.c

then i try installing apache2-mpm-prefork, but nothing changed

Gonzalo

Post by Scott Cain
Hmm, perhaps there is more than one error log; some time apache is
configured to produce error logs in different ways (though it's really
difficult for me to guess how that's setup for you). Again, if Apache is
giving the browser a 404 message, it should be logging that somewhere.
Scott
Sent from my iPad
Ok, i'm sorry, now cc'ed
Same as before, nothing about GBrowse in the error log tail
Gonzalo.

Post by Scott Cain
Hi Gonzalo,
Please keep the gbrowse mailing list cc'ed.
What is in your apache error log that mentions gbrowse (if there is a 404
message, there should be something in the error log).
Scott
Sent from my iPad
Thanks Scott!
when i go to localhost/gbrowse2 i got the html about the "Generic Genome
Browser, v2", the tutorials, and everything else.
the problem comes in http://localhost/cgi-bin/gb2/gbrowse/yeast/, there i got 404 =/
i also checked /usr/lib/cgi-bin/gb2 and all seems to be fine there.
Still nothing, any ideas?
Regards.

Post by Scott Cain
Hi Gonzalo,
The snippet of error log that you sent doesn't have anything to do with
GBrowse; it's just the normal messages one sees when apache is stopped and
started. What happens when you go to http://localhost/gbrowse2? What
about http://localhost/cgi-bin/gb2/gbrowse/yeast/? What do you see in
the browser, and what do you see in the error log?
By the way, changing the installed path of the cgi files to somewhere in
/var/www won't work unless you also modify the apache config, which would
be a pain to do. Instead, just make sure the scripts go into
/usr/lib/cgi-bin/gb2.
Scott
On Fri, Apr 4, 2014 at 3:49 PM, Gonzalo Sepulveda <

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Gonzalo Sepulveda

2014-04-07 13:38:55 UTC

Permalink

Ok, i'm sorry, now cc'ed
Same as before, nothing about GBrowse in the error log tail

Gonzalo.

Post by Scott Cain
Hi Gonzalo,
The snippet of error log that you sent doesn't have anything to do with
GBrowse; it's just the normal messages one sees when apache is stopped and
started. What happens when you go to http://localhost/gbrowse2? What
about http://localhost/cgi-bin/gb2/gbrowse/yeast/? What do you see in
the browser, and what do you see in the error log?
By the way, changing the installed path of the cgi files to somewhere in
/var/www won't work unless you also modify the apache config, which would
be a pain to do. Instead, just make sure the scripts go into
/usr/lib/cgi-bin/gb2.
Scott

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research