Quantcast

Suggestions for WebGBrowse

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Suggestions for WebGBrowse

Scott Cain
Hi Ram,

I just got done installing WebGBrowse on a Amazon cloud machine (at
http://cloud.gmod.org/) and have a few suggestions for improvements,
plus a few real bug reports.  Here goes:

Bugs:

* /usr/lib/cgi-bin/errorpage doesn't exist (but when tmp wasn't
writeable, that's what it looked for--and gave no useful message in
the apache error log that that was the problem).  WebGB.pm needs to be
fixed to look in the webgbrowse cgi-bin directory, and it would be
nice if an expressive error message went to the error log.

*  In generateConfigurationData2.0, you have

 -location => 'http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/' .
$timeStampDigest

but it needs to be something more like this:

 -location => 'http://'.$ENV{'SERVER_NAME'}.'/cgi-bin/gb2/gbrowse/' .
$timeStampDigest

* WebGBrowse assumes that the databases directory is in
/$HTDOCS/gbrowse2/databases, however, with the debian gbrowse package
installer (and possibly the current gbrowse installer), it goes in
/var/lib/gbrowse2.  Fixing this would, I believe, necessitate another
configuration parameter for the databases directory. I hard coded a
hack to fix this in the cloud instance.


INSTALL doc issues:

* Tell users to make /usr/lib/tmp (or whatever tmp is) world writable
(or writable by the webserver)

* need to make /etc/gbrowse2, /etc/gbrowse2/GBrowse.conf,
/var/lib/gbrowse2/databases (and presumably /etc/apache2/gbrowse.conf)
writable by the webserver

* $ENV{SERVER_NAME} is not set by default on the ubuntu server I'm
using.  You should provide a workaround--either by describing how to
set environment variable in apache or by letting the user set a config
parameter somewhere (I did it in the apache config, but I think
putting it in a config file would be better).

* Not thrilled with having to create /usr/lib/lib, /usr/lib/files and
/usr/lib/tmp (though that's what I did, since /usr/lib is ".." from
/usr/lib/cgi-bin, the debian/ubuntu default location for cgi-bin).


General comments:

Using this with a cloud instance is going to be tricky with all of the
tweaking that is necessary.  While I was be able to get it working
with the canonical instance (cloud.gmod.org), when someone clones it,
I believe it will break (actually, it will certainly break).  If all
of these things were stored in a "central" config file (perhaps in
/etc/webgbrowse), when it does break, it will be obvious for people to
know where to look.

Also, hard coding the email address for indiana.edu is probably not a
good idea--another configuration parameter.

Finally, nice work!  Even though I ran into problems, I still got it
installed and working in under an hour, so fixing the problems I ran
into were easy for me to fix (or at least hack :-) which to me is a
sign of quality work.

Thanks,
Scott


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

------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
_______________________________________________
Gmod-webgbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Suggestions for WebGBrowse

Ram Podicheti-2
Scott,
Thanks for the feedback. I will make the changes as you suggested.

Ram

-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Friday, February 10, 2012 2:40 PM
To: Podicheti, Ram
Cc: [hidden email]
Subject: Suggestions for WebGBrowse

Hi Ram,

I just got done installing WebGBrowse on a Amazon cloud machine (at
http://cloud.gmod.org/) and have a few suggestions for improvements, plus a few real bug reports.  Here goes:

Bugs:

* /usr/lib/cgi-bin/errorpage doesn't exist (but when tmp wasn't writeable, that's what it looked for--and gave no useful message in the apache error log that that was the problem).  WebGB.pm needs to be fixed to look in the webgbrowse cgi-bin directory, and it would be nice if an expressive error message went to the error log.

*  In generateConfigurationData2.0, you have

 -location => 'http://$ENV{'SERVER_NAME'}/cgi-bin/gb2/gbrowse/' .
$timeStampDigest

but it needs to be something more like this:

 -location => 'http://'.$ENV{'SERVER_NAME'}.'/cgi-bin/gb2/gbrowse/' .
$timeStampDigest

* WebGBrowse assumes that the databases directory is in /$HTDOCS/gbrowse2/databases, however, with the debian gbrowse package installer (and possibly the current gbrowse installer), it goes in /var/lib/gbrowse2.  Fixing this would, I believe, necessitate another configuration parameter for the databases directory. I hard coded a hack to fix this in the cloud instance.


INSTALL doc issues:

* Tell users to make /usr/lib/tmp (or whatever tmp is) world writable (or writable by the webserver)

* need to make /etc/gbrowse2, /etc/gbrowse2/GBrowse.conf, /var/lib/gbrowse2/databases (and presumably /etc/apache2/gbrowse.conf) writable by the webserver

* $ENV{SERVER_NAME} is not set by default on the ubuntu server I'm using.  You should provide a workaround--either by describing how to set environment variable in apache or by letting the user set a config parameter somewhere (I did it in the apache config, but I think putting it in a config file would be better).

* Not thrilled with having to create /usr/lib/lib, /usr/lib/files and /usr/lib/tmp (though that's what I did, since /usr/lib is ".." from /usr/lib/cgi-bin, the debian/ubuntu default location for cgi-bin).


General comments:

Using this with a cloud instance is going to be tricky with all of the tweaking that is necessary.  While I was be able to get it working with the canonical instance (cloud.gmod.org), when someone clones it, I believe it will break (actually, it will certainly break).  If all of these things were stored in a "central" config file (perhaps in /etc/webgbrowse), when it does break, it will be obvious for people to know where to look.

Also, hard coding the email address for indiana.edu is probably not a good idea--another configuration parameter.

Finally, nice work!  Even though I ran into problems, I still got it installed and working in under an hour, so fixing the problems I ran into were easy for me to fix (or at least hack :-) which to me is a sign of quality work.

Thanks,
Scott


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

------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
_______________________________________________
Gmod-webgbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-webgbrowse
Loading...