[Gmod-gbrowse] GBrowse Tutorial Set up receiving a Blank page

Discussion:

Annie Benitha

2017-05-27 22:44:58 UTC

Hi,

I tried setting the Gbrowse with the help of the tutorials and I ended up
getting the blank page,

[image: Inline image 2]

I checked the error logs and It says,

script not found or unable to stat: /usr/lib/cgi-bin/gb2/gbrowse2

I actually don't have a folder under that path with gbrowse2.

Could you please help me on how do I get this?

Thanks,
Annie

Scott Cain

2017-05-30 17:21:47 UTC

Permalink

Hi Annie,

The screenshot you included actually doesn't have a blank page, rather it
is missing all of the dynamically created images, which is a little
different. Given the message in your error log, I'm surprised you even got
that much. When you say that you don't have a folder with that path, what
exactly do you mean? Does /usr/lib/cgi-bin exist? What about gb2? If the
cgi-bin directory exists but gb2 does not, do you remember getting any
error messages when you installed GBrowse (and for that matter, how did you
install gbrowse?)?

Scott

Post by Annie Benitha
Hi,
I tried setting the Gbrowse with the help of the tutorials and I ended up
getting the blank page,
[image: Inline image 2]
I checked the error logs and It says,
script not found or unable to stat: /usr/lib/cgi-bin/gb2/gbrowse2
I actually don't have a folder under that path with gbrowse2.
Could you please help me on how do I get this?
Thanks,
Annie
------------------------------------------------------------
------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
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

2017-05-31 16:53:41 UTC

Permalink

Hi Annie,

Please keep the gbrowse list cc'ed in your responses.

How did you uninstall/install gbrowse?

Scott

Hi Scott,
I thought something was wrong , so I uninstalled everything, and now I
don't get /etc/gbrowse2 , I only get /etc/gbrowse and I get
/usr/lib/cgi-bin/gbrowse this hierarchy was created.
Is there a reason why gbrowse2 folder is not being created at all?
Thanks,
Annie

Post by Scott Cain
Hi Annie,
The screenshot you included actually doesn't have a blank page, rather it
is missing all of the dynamically created images, which is a little
different. Given the message in your error log, I'm surprised you even got
that much. When you say that you don't have a folder with that path, what
exactly do you mean? Does /usr/lib/cgi-bin exist? What about gb2? If the
cgi-bin directory exists but gb2 does not, do you remember getting any
error messages when you installed GBrowse (and for that matter, how did you
install gbrowse?)?
Scott

Post by Annie Benitha
Hi,
I tried setting the Gbrowse with the help of the tutorials and I ended
up getting the blank page,
[image: Inline image 2]
I checked the error logs and It says,
script not found or unable to stat: /usr/lib/cgi-bin/gb2/gbrowse2
I actually don't have a folder under that path with gbrowse2.
Could you please help me on how do I get this?
Thanks,
Annie
------------------------------------------------------------
------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
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
<(216)%20392-3087>
Ontario Institute for Cancer Research

Scott Cain

2017-05-31 19:40:31 UTC

Permalink

Hi Annie,

I was not familiar with that page--I don't even know who wrote it. I added
a comment to it to make sure users don't think it is a "definitive" list.
The important part of the question that you didn't answer was how did you
install GBrowse in the first place?

Thanks,
Scott

HI,
I followed the procedure from this page.
http://gmod.org/wiki/GBrowse_2.0_Install_Paths.
Thanks,
Annie

Post by Scott Cain
Hi Annie,
Please keep the gbrowse list cc'ed in your responses.
How did you uninstall/install gbrowse?
Scott

Post by Scott Cain
Hi Annie,
The screenshot you included actually doesn't have a blank page, rather
it is missing all of the dynamically created images, which is a little
different. Given the message in your error log, I'm surprised you even got
that much. When you say that you don't have a folder with that path, what
exactly do you mean? Does /usr/lib/cgi-bin exist? What about gb2? If the
cgi-bin directory exists but gb2 does not, do you remember getting any
error messages when you installed GBrowse (and for that matter, how did you
install gbrowse?)?
Scott

Post by Annie Benitha
Hi,
I tried setting the Gbrowse with the help of the tutorials and I ended
up getting the blank page,
[image: Inline image 2]
I checked the error logs and It says,
script not found or unable to stat: /usr/lib/cgi-bin/gb2/gbrowse2
I actually don't have a folder under that path with gbrowse2.
Could you please help me on how do I get this?
Thanks,
Annie
------------------------------------------------------------
------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
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
<(216)%20392-3087>
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
<(216)%20392-3087>
Ontario Institute for Cancer Research

Scott Cain

2017-05-31 20:38:09 UTC

Permalink

Hi Annie,

So you installed it both via cpan and apt-get? That's likely to result in
quite a mess. :-/ Then deleting some but presumably not all of the files
installed might compound things, since apt-get will install GBrowse in
considerably less obvious places (so much so that I can never remember
where they go).

I assume you're using Ubuntu; what version? In some versions of Ubuntu the
web docroot is /var/www, not /var/www/html, which might explain why you
can't find the gbrowse2 folder, though that strikes me as somewhat
unlikely, since I think that change was made quite some time ago (several
years).

If it were me and it was an option, I would wipe my install of Ubuntu,
install it again, then follow the "prereqs only" instructions on the
GBrowse ubuntu page, then install GBrowse via cpan, of course, making sure
to note any error messages along the way. I'm sorry that I can't be more
help at this point via email, but it is extremely difficult to debug
installation issues like this without access to the machine.

Good luck,
Scott

Hi Scott,
I did numerous things.
1) sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
2)http://gmod.org/wiki/GBrowse_Ubuntu_HOWTO - followed all steps of this.
Thats it.
But I dont find the /var/www/html/gbrowse2 folder at all.
Thanks,
Annie

Post by Scott Cain
Hi Annie,
I was not familiar with that page--I don't even know who wrote it. I
added a comment to it to make sure users don't think it is a "definitive"
list. The important part of the question that you didn't answer was how
did you install GBrowse in the first place?
Thanks,
Scott

HI,
I followed the procedure from this page.
http://gmod.org/wiki/GBrowse_2.0_Install_Paths.
Thanks,
Annie

Post by Scott Cain
Hi Annie,
Please keep the gbrowse list cc'ed in your responses.
How did you uninstall/install gbrowse?
Scott

Post by Scott Cain
Hi Annie,
The screenshot you included actually doesn't have a blank page,
rather it is missing all of the dynamically created images, which is a
little different. Given the message in your error log, I'm surprised you
even got that much. When you say that you don't have a folder with that
path, what exactly do you mean? Does /usr/lib/cgi-bin exist? What about
gb2? If the cgi-bin directory exists but gb2 does not, do you remember
getting any error messages when you installed GBrowse (and for that matter,
how did you install gbrowse?)?
Scott
On Sat, May 27, 2017 at 6:44 PM, Annie Benitha <

Post by Annie Benitha
Hi,
I tried setting the Gbrowse with the help of the tutorials and I
ended up getting the blank page,
[image: Inline image 2]
I checked the error logs and It says,
script not found or unable to stat: /usr/lib/cgi-bin/gb2/gbrowse2
I actually don't have a folder under that path with gbrowse2.
Could you please help me on how do I get this?
Thanks,
Annie
------------------------------------------------------------
------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
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
<(216)%20392-3087>
Ontario Institute for Cancer Research

--
------------------------------------------------------------
------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
<(216)%20392-3087>
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
<(216)%20392-3087>
Ontario Institute for Cancer Research

Annie Benitha

2017-05-31 21:56:14 UTC

Permalink

Hi Scott,

I was thinking the same, would Install Ubuntu and try again.
And the only folder in /var/www is the html folder and inside this is the
index.html, but previously the folder /var/www/html/gbrowse2 was installed.

Anyway I will install this again.

Thanks,
Annie

Post by Scott Cain
Hi Annie,
So you installed it both via cpan and apt-get? That's likely to result in
quite a mess. :-/ Then deleting some but presumably not all of the files
installed might compound things, since apt-get will install GBrowse in
considerably less obvious places (so much so that I can never remember
where they go).
I assume you're using Ubuntu; what version? In some versions of Ubuntu
the web docroot is /var/www, not /var/www/html, which might explain why you
can't find the gbrowse2 folder, though that strikes me as somewhat
unlikely, since I think that change was made quite some time ago (several
years).
If it were me and it was an option, I would wipe my install of Ubuntu,
install it again, then follow the "prereqs only" instructions on the
GBrowse ubuntu page, then install GBrowse via cpan, of course, making sure
to note any error messages along the way. I'm sorry that I can't be more
help at this point via email, but it is extremely difficult to debug
installation issues like this without access to the machine.
Good luck,
Scott

HI,
I followed the procedure from this page.
http://gmod.org/wiki/GBrowse_2.0_Install_Paths.
Thanks,
Annie

Post by Scott Cain
Hi Annie,
Please keep the gbrowse list cc'ed in your responses.
How did you uninstall/install gbrowse?
Scott

Hi Scott,
I thought something was wrong , so I uninstalled everything, and now
I don't get /etc/gbrowse2 , I only get /etc/gbrowse and I get
/usr/lib/cgi-bin/gbrowse this hierarchy was created.
Is there a reason why gbrowse2 folder is not being created at all?
Thanks,
Annie

Post by Scott Cain
Hi Annie,
The screenshot you included actually doesn't have a blank page,
rather it is missing all of the dynamically created images, which is a
little different. Given the message in your error log, I'm surprised you
even got that much. When you say that you don't have a folder with that
path, what exactly do you mean? Does /usr/lib/cgi-bin exist? What about
gb2? If the cgi-bin directory exists but gb2 does not, do you remember
getting any error messages when you installed GBrowse (and for that matter,
how did you install gbrowse?)?
Scott
On Sat, May 27, 2017 at 6:44 PM, Annie Benitha <

Post by Annie Benitha
Hi,
I tried setting the Gbrowse with the help of the tutorials and I
ended up getting the blank page,
[image: Inline image 2]
I checked the error logs and It says,
script not found or unable to stat: /usr/lib/cgi-bin/gb2/gbrowse2
I actually don't have a folder under that path with gbrowse2.
Could you please help me on how do I get this?
Thanks,
Annie
------------------------------------------------------------
------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
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
<(216)%20392-3087>
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
<(216)%20392-3087>
Ontario Institute for Cancer Research