gbrowse is killing me

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gbrowse is killing me

Fernando Rodriguez
Hi,

It wasn't the first time I've installed gbrowser (previous attempts were good). But I just update (format) my desk computer and the installation of gbrowse is killing me.
So I've started with Biolinux 8 distribution; nothing came out of my browser. All paths seems clear, all prerequisites installed (apache working, etc etc). Well, there people complaining about Biolinux 8 distribution an gbrowse....lets re-format and install just ubuntu 14.04 LTS.....same troubles
...install apache, bioperl and download gbrowse2 (I think it is 2.55) from CPAN (also try with binary source)

The most I could do was getting a forbidden page on http://localhost/gb2/gbrowse/yeast.
And the frustrating thing is on the other side of my desk I have my laptop with gbrowse (2.42) well installed on ubuntu 12.04....looking and comparing folder by folder, file by file. Even with the tips I get at the Summer school in 2013, I am not able of doing it :(

Instead of losing time with details, could it be better to run it on a different os (fedora, centos)? Any other input would be appreciated. Thanks

--
Fernando Rodriguez, Ph.D.
Josephine Bay Paul Center for
Comparative Molecular Biology and Evolution
Marine Biological Laboratory
Woods Hole, MA 02543
Tel. (508) 289-7510
Fax: (508) 457-4727
[hidden email]


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Re: gbrowse is killing me

Allan Kamau
Check the apache logs for permission errors.
It is also likely that you have SELinux enforced and preventing some process from running.

Allan.

On Sat, Mar 21, 2015 at 4:47 AM, Fernando Rodriguez <[hidden email]> wrote:
Hi,

It wasn't the first time I've installed gbrowser (previous attempts were good). But I just update (format) my desk computer and the installation of gbrowse is killing me.
So I've started with Biolinux 8 distribution; nothing came out of my browser. All paths seems clear, all prerequisites installed (apache working, etc etc). Well, there people complaining about Biolinux 8 distribution an gbrowse....lets re-format and install just ubuntu 14.04 LTS.....same troubles
...install apache, bioperl and download gbrowse2 (I think it is 2.55) from CPAN (also try with binary source)

The most I could do was getting a forbidden page on http://localhost/gb2/gbrowse/yeast.
And the frustrating thing is on the other side of my desk I have my laptop with gbrowse (2.42) well installed on ubuntu 12.04....looking and comparing folder by folder, file by file. Even with the tips I get at the Summer school in 2013, I am not able of doing it :(

Instead of losing time with details, could it be better to run it on a different os (fedora, centos)? Any other input would be appreciated. Thanks

--
Fernando Rodriguez, Ph.D.
Josephine Bay Paul Center for
Comparative Molecular Biology and Evolution
Marine Biological Laboratory
Woods Hole, MA 02543
Tel. (508) 289-7510
Fax: (508) 457-4727
[hidden email]


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by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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Re: gbrowse is killing me

Raymond Wan
In reply to this post by Fernando Rodriguez

Hi Fernando,


Quoting Fernando Rodriguez <[hidden email]>:

> The most I could do was getting a forbidden page on
> http://localhost/gb2/gbrowse/yeast .
> And the frustrating thing is on the other side of my desk I have my laptop
> with gbrowse (2.42) well installed on ubuntu 12.04....looking and comparing
> folder by folder, file by file. Even with the tips I get at the Summer school
> in 2013, I am not able of doing it :(
>
> Instead of losing time with details, could it be better to run it on a
> different os (fedora, centos)? Any other input would be appreciated. Thanks


I'm not too sure what others think, but personally, I don't think installing
another OS would help.  Each OS has different defaults and maybe one
distribution specific for bioinformatics might have many things set for GBrowse
whereas a more general distribution has users doing non-bioinformatics things
(i.e., running a Wiki, etc.).  And thus, the latter one might be harder to get
"right".

I would suggest you pick a distribution which has the most information or people
to ask help from (including people around you).  Because even if you finish
struggling with GBrowse, you may want to set up other things.

More specific to GBrowse, I think you should check things off one at a time.
Can you confirm the Apache web server is up?  Can you access some parts of the
web server (i.e., does http://localhost/ work?) and not others?  And so on.

I don't know what notes you got for the 2013 Summer School, but Ubuntu 14.04 or
14.10 made a big change (if I remember correctly) and that was moving web pages
from /var/www to /var/www/html/ by default.  You can change it back, but it's
something that both Ubuntu and Debian is moving towards (following on the
footsteps of Red Hat / Fedora, I *think*).  So, I wouldn't do a directory by
directory comparision; instead, try to look up information specific to 14.04.
There are minor changes from version to version and a diretory move is "minor"
but has a big impact.

That's all that comes to mind...hope it helps!

Ray

PS:  The DocumentRoot is set in /etc/apache2/sites-enabled/000-default.conf
(which is symlinked elsewhere).  However, I don't recommend you change its
value to /var/www/ .  If you upgrade, it will change it back again.  I'm not
sure if the GBrowse package for Ubuntu has this fixed; but if you are
installing from source, you should be careful of this.

PPS:  And agree with Allan's comment about looking at the Apache logs in
/var/log/apache2 (by default).




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