[Gmod-gbrowse] help regarding gbrowse

Hi Umay,

Can you please tell us what you done and where you think the process has failed? For instance, what do you see when you go to the built in sample yeast data set?

Scott

Sent from my iPhone

Post by umay kulsum
I have been trying to install and invoke GBrowse since a month but to
no result....
can someone help me regarding the installation process.
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Scott Cain

2014-09-17 14:17:06 UTC

Umay,

Please "reply-all" so that your replies stay on the GBrowse mailing list.

A few things:

The url you are using is not correct; it should be
http://localhost/cgi-bin/gb2/gbrowse/yeast. This is linked to from
http://localhost/gbrowse2/

I don't know why you have two yeast_chr1+2 directories, but only one of
them will work. The typical configuration would be for the one in
/var/lib/gbrowse2/databases to work.

The cgi-bin directory is not in the /var/www directory when apache is
typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it is in your
case.

Scott

I have installed GBrowse using the command in ubuntu 14.04
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
etc/gbrowse2/GBrowse.conf
var/www/gbrowse2/databases where I have the yeast_chr1+2 folder with
my own data files
usr/lib/cgi-bin/gb2
var/lib/gbrowse2/databases/yeast_chr1+2 with other files
but still the url http://localhost/cgi-bin/gbrowse2/yeast shows the
following url was not found on the server
where is the cgi-bin mentioned in the url located when it is not in
/var/www/

Hi
I have installed GBrowse using the command in ubuntu 14.04
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
but when I point my browser to
http://localhost/cgi-bin/gbrowse2/yeast, it shows the following url is
not found on this server..
where is the cgi-bin mentioned in the url located when it is not in

/var/www/

Post by Scott Cain
Hi Umay,
Can you please tell us what you done and where you think the process

has failed? For instance, what do you see when you go to the built in
sample yeast data set?

Post by Scott Cain
Scott
Sent from my iPhone

Post by umay kulsum
I have been trying to install and invoke GBrowse since a month but to
no result....
can someone help me regarding the installation process.

------------------------------------------------------------------------------

Post by umay kulsum
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.

http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk

Post by umay kulsum
_______________________________________________
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

umay kulsum

2014-09-18 03:03:04 UTC

hi
I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but again
its the same the requested url is not found on the server...
what should I do??
where am I going wrong??
can you please tell me how can I start from scratch that is uninstall
and then reinstall....

Post by Scott Cain
Umay,
Please "reply-all" so that your replies stay on the GBrowse mailing list.
The url you are using is not correct; it should be
http://localhost/cgi-bin/gb2/gbrowse/yeast. This is linked to from
http://localhost/gbrowse2/
I don't know why you have two yeast_chr1+2 directories, but only one of them
will work. The typical configuration would be for the one in
/var/lib/gbrowse2/databases to work.
The cgi-bin directory is not in the /var/www directory when apache is
typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it is in your
case.
Scott

Post by Scott Cain
Hi Umay,
Can you please tell us what you done and where you think the process
has failed? For instance, what do you see when you go to the built in
sample yeast data set?
Scott
Sent from my iPhone

Scott Cain

2014-09-18 05:04:58 UTC

Hi Umay,

What does it say in the apache error log? If you're getting a message about a file not being found, it will record where it was looking for the file. The error log is in /var/log/apache2. The most recent message is at the end of the file.

Scott

Sent from my iPhone

Post by umay kulsum
hi
I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but again
its the same the requested url is not found on the server...
what should I do??
where am I going wrong??
can you please tell me how can I start from scratch that is uninstall
and then reinstall....

umay kulsum

2014-09-18 05:55:46 UTC

The apache error log shows :

[Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766] AH00094:
Command line: '/usr/sbin/apache2'

This is the last comment in /var/log/apache2/error.log...... it shows
nothing regarding the files not found

In the access.log file the last comment is :

127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
/cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"

Post by Scott Cain
Hi Umay,
What does it say in the apache error log? If you're getting a message about a file not being found, it will record where it was looking for the file. The error log is in /var/log/apache2. The most recent message is at the end of the file.
Scott
Sent from my iPhone

umay kulsum

2014-09-18 06:15:29 UTC

whenever we write localhost it looks for files in /var/www/html
so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www

Post by umay kulsum
Command line: '/usr/sbin/apache2'
This is the last comment in /var/log/apache2/error.log...... it shows
nothing regarding the files not found
127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
/cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"

Scott Cain

2014-09-18 14:07:27 UTC

Hi Umay,

I suspect you are using Ubuntu 14.04 (you may have already told me that--I
don't remember). While working recently on some minor bug fixes for
GBrowse, we discovered that when Ubuntu 14.04 was released, they
dramatically rearranged the file structure for system files, which broke
the GBrowse installer. The easiest way to install GBrowse correctly at the
moment is to get a GitHub checkout of the current source and install that
way. It's fairly straight forward; this is what you do:

git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install

After doing that you should be able to go to http://localhost/gbrowse2 though
the links for sample data sets are written assuming you have fastcgi
installed (which is a good idea to use, because it makes things faster),
but if you don't have fastcgi, you should still be able to go to
http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset. If
that works, you should be able to proceed with the tutorial as well.

Post by umay kulsum
whenever we write localhost it looks for files in /var/www/html
so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www

Post by Scott Cain
Hi Umay,
What does it say in the apache error log? If you're getting a message

about a file not being found, it will record where it was looking for the
file. The error log is in /var/log/apache2. The most recent message is at
the end of the file.

Post by Scott Cain
Scott
Sent from my iPhone

Post by Scott Cain
Umay,
Please "reply-all" so that your replies stay on the GBrowse mailing

list.

Post by Scott Cain
The url you are using is not correct; it should be
http://localhost/cgi-bin/gb2/gbrowse/yeast. This is linked to from
http://localhost/gbrowse2/
I don't know why you have two yeast_chr1+2 directories, but only one

of them

Post by Scott Cain
will work. The typical configuration would be for the one in
/var/lib/gbrowse2/databases to work.
The cgi-bin directory is not in the /var/www directory when apache is
typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it is

in your

Post by Scott Cain
case.
Scott

url is

not found on this server..
where is the cgi-bin mentioned in the url located when it is not in
/var/www/

Post by Scott Cain
Hi Umay,
Can you please tell us what you done and where you think the

process

Post by Scott Cain
has failed? For instance, what do you see when you go to the

built in

Post by Scott Cain
sample yeast data set?
Scott
Sent from my iPhone

Post by umay kulsum
I have been trying to install and invoke GBrowse since a month

but to

Post by umay kulsum
no result....
can someone help me regarding the installation process.

------------------------------------------------------------------------------

Post by umay kulsum
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.

http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk

Post by umay kulsum
_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------

Post by Scott Cain
Scott Cain, Ph. D. scott at

scottcain dot

Post by Scott Cain
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Scott Cain

2014-09-22 12:06:55 UTC

Hi Umay,

I don't really know what the problem is--my guess is that there is a
network problem. Can you try from a different network? Can you clone
other things from git but just not GBrowse (I would find that pretty
strange if it were the case)? Also, in case there is a problem with any of
the software packages you are using, you should probably run

sudo apt-get update
sudo apt-get upgrade

to make sure your system is up to date.

Scott

Hi
when I do
git clone https://github.com/GMOD/GBrowse.git
Cloning into 'GBrowse'...
gnutls_handshake() failed: A TLS packet with unexpected length was
received.

Post by Scott Cain
Hi Umay,
I suspect you are using Ubuntu 14.04 (you may have already told me

that--I

Post by Scott Cain
don't remember). While working recently on some minor bug fixes for
GBrowse, we discovered that when Ubuntu 14.04 was released, they
dramatically rearranged the file structure for system files, which broke

the

Post by Scott Cain
GBrowse installer. The easiest way to install GBrowse correctly at the
moment is to get a GitHub checkout of the current source and install that
git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install
After doing that you should be able to go to http://localhost/gbrowse2
though the links for sample data sets are written assuming you have

fastcgi

Post by Scott Cain
installed (which is a good idea to use, because it makes things faster),

but

Post by Scott Cain
if you don't have fastcgi, you should still be able to go to
http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset. If

that

Post by Scott Cain
works, you should be able to proceed with the tutorial as well.

Post by umay kulsum
whenever we write localhost it looks for files in /var/www/html
so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www

Post by Scott Cain
Hi Umay,
What does it say in the apache error log? If you're getting a

message

Post by Scott Cain
about a file not being found, it will record where it was looking

for the

Post by Scott Cain
file. The error log is in /var/log/apache2. The most recent message

is at

Post by Scott Cain
the end of the file.
Scott
Sent from my iPhone

Post by umay kulsum
hi
I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also but

again

Post by umay kulsum
its the same the requested url is not found on the server...
what should I do??
where am I going wrong??
can you please tell me how can I start from scratch that is

uninstall

Post by umay kulsum
and then reinstall....

from

Post by Scott Cain
http://localhost/gbrowse2/
I don't know why you have two yeast_chr1+2 directories, but only

one

Post by Scott Cain
of them
will work. The typical configuration would be for the one in
/var/lib/gbrowse2/databases to work.
The cgi-bin directory is not in the /var/www directory when apache

Post by Scott Cain
typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it is in your
case.
Scott

On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum <
I have installed GBrowse using the command in ubuntu 14.04
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
etc/gbrowse2/GBrowse.conf
var/www/gbrowse2/databases where I have the yeast_chr1+2 folder

with

my own data files
usr/lib/cgi-bin/gb2
var/lib/gbrowse2/databases/yeast_chr1+2 with other files
but still the url http://localhost/cgi-bin/gbrowse2/yeast shows

the

following url was not found on the server
where is the cgi-bin mentioned in the url located when it is not

/var/www/
On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum <

url

is
not found on this server..
where is the cgi-bin mentioned in the url located when it is not

/var/www/

On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain <
Hi Umay,
Can you please tell us what you done and where you think the process
has failed? For instance, what do you see when you go to the
built in
sample yeast data set?
Scott
Sent from my iPhone

On Sep 11, 2014, at 11:41 PM, umay kulsum <
I have been trying to install and invoke GBrowse since a month
but to
no result....
can someone help me regarding the installation process.

------------------------------------------------------------------------------

Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.

http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk

_______________________________________________
Gmod-gbrowse mailing list
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------

Post by Scott Cain
Scott Cain, Ph. D. scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Post by Scott Cain
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain

dot

Post by Scott Cain
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

umay kulsum

2014-09-23 03:35:56 UTC

Hi

Thank you scott....got GBrowse installed with git clone...
example database of yeast is also working properly...

but now I have created my own conf file as 114635370.conf in
etc/gbrowse2/gbrowse.conf folder but when I run
http://localhost/cgi-bin/gb2/gbrowse/114635370 it gives the result of
yeast but not my own file
why is it so and what can I do for that??

my conf file is as follows:

[GENERAL]
description = motifs of 114635370protein
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir '/var/www/html/gbrowse2/databases/1/1/4/114635370/'

plugins = BatchDumper FastaDumper
gbrowse root = gbrowse
stylesheet = gbrowse.css
buttons = images/buttons
js = js
tmpimages = tmp
region segment = 500
initial landmark = 114635370
balloon tips = 1
drag and drop = 1
cache time = 1
link = AUTO
image widths = 450 640 800 1024
hilite fill = beige
hilite outline = red
default width = 800
default features = 114635370
max segment = 500
default segment = 50
zoom levels = 50 100 200 1000 2000 5000 10000 20000 40000 100000
200000 500000 1000000
show sources = 1
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
examples = 114635370
automatic classes = 114635370

[protein]
feature = protein
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 1
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See protein
details</a></th></tr>
<tr align='left'><th><a
href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
NCBI</a></th></tr>
</table>

key = protein
[pattern]
feature = pattern
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 1
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See gene
details</a></th></tr>
<tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
<tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
</table>

key = pattern

[profile]
feature = profile
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 0
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
<tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
</table>
key = profile

Post by Scott Cain
Hi Umay,
I don't really know what the problem is--my guess is that there is a network
problem. Can you try from a different network? Can you clone other things
from git but just not GBrowse (I would find that pretty strange if it were
the case)? Also, in case there is a problem with any of the software
packages you are using, you should probably run
sudo apt-get update
sudo apt-get upgrade
to make sure your system is up to date.
Scott

Hi
when I do
git clone https://github.com/GMOD/GBrowse.git
Cloning into 'GBrowse'...
gnutls_handshake() failed: A TLS packet with unexpected length was
received.

Post by Scott Cain
Hi Umay,
I suspect you are using Ubuntu 14.04 (you may have already told me that--I
don't remember). While working recently on some minor bug fixes for
GBrowse, we discovered that when Ubuntu 14.04 was released, they
dramatically rearranged the file structure for system files, which broke the
GBrowse installer. The easiest way to install GBrowse correctly at the
moment is to get a GitHub checkout of the current source and install that
git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install
After doing that you should be able to go to http://localhost/gbrowse2
though the links for sample data sets are written assuming you have fastcgi
installed (which is a good idea to use, because it makes things faster), but
if you don't have fastcgi, you should still be able to go to
http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset. If that
works, you should be able to proceed with the tutorial as well.

Post by umay kulsum
whenever we write localhost it looks for files in /var/www/html
so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www

Post by Scott Cain
Hi Umay,
What does it say in the apache error log? If you're getting a message
about a file not being found, it will record where it was looking for the
file. The error log is in /var/log/apache2. The most recent message is at
the end of the file.
Scott
Sent from my iPhone

Post by Scott Cain
Umay,
Please "reply-all" so that your replies stay on the GBrowse mailing
list.
The url you are using is not correct; it should be
http://localhost/cgi-bin/gb2/gbrowse/yeast. This is linked to from
http://localhost/gbrowse2/
I don't know why you have two yeast_chr1+2 directories, but only one
of them
will work. The typical configuration would be for the one in
/var/lib/gbrowse2/databases to work.
The cgi-bin directory is not in the /var/www directory when apache is
typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it is
in your
case.
Scott

On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
I have installed GBrowse using the command in ubuntu 14.04
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
etc/gbrowse2/GBrowse.conf
var/www/gbrowse2/databases where I have the yeast_chr1+2 folder with
my own data files
usr/lib/cgi-bin/gb2
var/lib/gbrowse2/databases/yeast_chr1+2 with other files
but still the url http://localhost/cgi-bin/gbrowse2/yeast shows the
following url was not found on the server
where is the cgi-bin mentioned in the url located when it is not in
/var/www/
On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum

Hi
I have installed GBrowse using the command in ubuntu 14.04
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
but when I point my browser to
http://localhost/cgi-bin/gbrowse2/yeast, it shows the following
url
is
not found on this server..
where is the cgi-bin mentioned in the url located when it is not in
/var/www/

On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
Hi Umay,
Can you please tell us what you done and where you think the
process
has failed? For instance, what do you see when you go to the
built in
sample yeast data set?
Scott
Sent from my iPhone

On Sep 11, 2014, at 11:41 PM, umay kulsum
I have been trying to install and invoke GBrowse since a month
but to
no result....
can someone help me regarding the installation process.
------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
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

2014-09-23 13:22:29 UTC

Hi Umay,

I'm glad you've gotten it working.

What you're describing with asking for one configuration and getting
another is what happens when there is a problem with the configuration that
you want. I don't see anything obvious with the configuration you pasted
into the email, but my eyes aren't as good a configuration parser as
GBrowse. A few questions:

Do you see anything in the apache error log that indicates that there is a
problem?

Did you add an entry for the new configuration file to
/etc/gbrowse/GBrowse.conf?

Scott

Post by umay kulsum
Hi
Thank you scott....got GBrowse installed with git clone...
example database of yeast is also working properly...
but now I have created my own conf file as 114635370.conf in
etc/gbrowse2/gbrowse.conf folder but when I run
http://localhost/cgi-bin/gb2/gbrowse/114635370 it gives the result of
yeast but not my own file
why is it so and what can I do for that??
[GENERAL]
description = motifs of 114635370protein
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir '/var/www/html/gbrowse2/databases/1/1/4/114635370/'
plugins = BatchDumper FastaDumper
gbrowse root = gbrowse
stylesheet = gbrowse.css
buttons = images/buttons
js = js
tmpimages = tmp
region segment = 500
initial landmark = 114635370
balloon tips = 1
drag and drop = 1
cache time = 1
link = AUTO
image widths = 450 640 800 1024
hilite fill = beige
hilite outline = red
default width = 800
default features = 114635370
max segment = 500
default segment = 50
zoom levels = 50 100 200 1000 2000 5000 10000 20000 40000 100000
200000 500000 1000000
show sources = 1
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
examples = 114635370
automatic classes = 114635370
[protein]
feature = protein
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 1
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See protein
details</a></th></tr>
<tr align='left'><th><a
href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
NCBI</a></th></tr>
</table>
key = protein
[pattern]
feature = pattern
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 1
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See gene
details</a></th></tr>
<tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
<tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
</table>
key = pattern
[profile]
feature = profile
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 0
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
<tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
</table>
key = profile

Post by Scott Cain
Hi Umay,
I don't really know what the problem is--my guess is that there is a

network

Post by Scott Cain
problem. Can you try from a different network? Can you clone other

things

Post by Scott Cain
from git but just not GBrowse (I would find that pretty strange if it

were

Post by Scott Cain
the case)? Also, in case there is a problem with any of the software
packages you are using, you should probably run
sudo apt-get update
sudo apt-get upgrade
to make sure your system is up to date.
Scott

Hi
when I do
git clone https://github.com/GMOD/GBrowse.git
Cloning into 'GBrowse'...
gnutls_handshake() failed: A TLS packet with unexpected length was
received.

broke

Post by Scott Cain
the
GBrowse installer. The easiest way to install GBrowse correctly at

the

Post by Scott Cain
moment is to get a GitHub checkout of the current source and install that
git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install
After doing that you should be able to go to

http://localhost/gbrowse2

Post by Scott Cain
though the links for sample data sets are written assuming you have fastcgi
installed (which is a good idea to use, because it makes things

faster),

Post by Scott Cain
but
if you don't have fastcgi, you should still be able to go to
http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.

Post by Scott Cain
that
works, you should be able to proceed with the tutorial as well.

Post by umay kulsum
whenever we write localhost it looks for files in /var/www/html
so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www

Post by umay kulsum
[Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766]
Command line: '/usr/sbin/apache2'
This is the last comment in /var/log/apache2/error.log...... it

shows

Post by umay kulsum
nothing regarding the files not found
127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
/cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"

Post by Scott Cain
Hi Umay,
What does it say in the apache error log? If you're getting a message
about a file not being found, it will record where it was looking for the
file. The error log is in /var/log/apache2. The most recent

message

Post by Scott Cain
is at
the end of the file.
Scott
Sent from my iPhone

On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain <
Umay,
Please "reply-all" so that your replies stay on the GBrowse mailing
list.
The url you are using is not correct; it should be
http://localhost/cgi-bin/gb2/gbrowse/yeast. This is linked to from
http://localhost/gbrowse2/
I don't know why you have two yeast_chr1+2 directories, but only one
of them
will work. The typical configuration would be for the one in
/var/lib/gbrowse2/databases to work.
The cgi-bin directory is not in the /var/www directory when

apache

is
typically configured for ubuntu; it's in /usr/lib/cgi-bin, as it is
in your
case.
Scott

shows

the
following url was not found on the server
where is the cgi-bin mentioned in the url located when it is

not

in
/var/www/
On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum

following

url
is
not found on this server..
where is the cgi-bin mentioned in the url located when it is

not

in
/var/www/

On Sep 11, 2014, at 11:41 PM, umay kulsum
I have been trying to install and invoke GBrowse since a

month

but to
no result....
can someone help me regarding the installation process.

------------------------------------------------------------------------------

Want excitement?
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When you want reliability, choose Perforce
Perforce version control. Predictably reliable.

http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk

_______________________________________________
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

------------------------------------------------------------------------

Post by Scott Cain
Scott Cain, Ph. D. scott at

scottcain

Post by Scott Cain
dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain

dot

Post by Scott Cain
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Scott Cain

2014-09-24 15:03:28 UTC

Hi Umay,

That message at the top of the screenshot you sent is the full error
message. The first line of it has the source of the problem. It can't
open the file at /var/lib/gbrowse2/databases/1...... Does that directory
exist and does the webserver have permission to open it? Probably the best
thing to do is to change ownership of that directory to the user that runs
the webserver:

sudo chown -R www-data:www-data /var/lib/gbrowse2/databases/*

If you're making frequent edits in the databases directories (like when
you're doing the tutorial), you can just make the directory you're working
on world writeable, so that the webserver and you can both write files in
the directory without sudo. Of course, this is considerably less secure:

sudo chmod -R a+w /var/lib/gbrowse2/databases/nameofdatabase

Scott

hi Scott
<?php
$ourFileName = "/etc/gbrowse2/gbrowse.conf/".10190714.".conf";
$ourFileHandle = fopen($ourFileName, 'w') or die("can't open file");
$p="[GENERAL]
description = motifs of ".21105857."protein
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir '/var/www/html/gbrowse2/databases/10190714'
plugins = BatchDumper FastaDumper
gbrowse root = gbrowse
stylesheet = gbrowse.css
buttons = images/buttons
js = js
tmpimages = tmp
region segment = 500
initial landmark = \".21105857.\"
balloon tips = 1
drag and drop = 1
cache time = 1
link = AUTO
image widths = 450 640 800 1024
hilite fill = beige
hilite outline = red
default width = 800
default features = \".21105857.\"
max segment = 500
default segment = 50
zoom levels = 50 100 200 1000 2000 5000 10000 20000 40000 100000
200000 500000 1000000
show sources = 1
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
examples =\".21105857.\"
automatic classes = \".21105857.\"
[protein]
feature = protein
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 1
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align=\"left\"><br>
This protein brought to you by <a
href=\"http://www.expasy.ch\">EXPASY</a>.</th>
<th bgcolor=\"cyan\">Gene </th>
</tr>
<tr align='left'><th><a
href=\"/cgi-bin/gbrowse_details/motif?name=\">See protein
details</a></th></tr>
<tr align='left'><th><a
href=\"http://www.ncbi.nlm.nih.gov/protein/\".21105857."">Go to
NCBI</a></th></tr>
</table>
key = protein
[pattern]
feature = pattern
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 1
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align=\"left\"><br>
This protein brought to you by <a
href=\"http://www.expasy.ch\">EXPASY</a>.</th>
<th bgcolor=\"cyan\">Gene </th>
</tr>
<tr align='left'><th><a
href=\"/cgi-bin/gbrowse_details/motif?name=\">See gene
details</a></th></tr>
<tr align='left'><th><a
href=\"http://en.wikipedia.org/wiki/Special:Search?search=\">Ask
Wikipedia about </a></th></tr>
<tr align='left'><th><a
href=\"http://www.google.com/search?q=\">Ask Google about
</a></th></tr>
</table>
key = pattern
[profile]
feature = profile
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 0
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align=\"left\"><br>
This protein brought to you by <a
href=\"http://www.expasy.ch\">EXPASY</a>.</th>
<th bgcolor=\"cyan\">Gene </th>
</tr>
<tr align='left'><th><a
href=\"http://en.wikipedia.org/wiki/Special:Search?search=/\">Ask
Wikipedia about </a></th></tr>
<tr align='left'><th><a
href=\"http://www.google.com/search?q=\">Ask Google about
</a></th></tr>
</table>
key = profile";
fwrite($ourFileHandle, $p);
$url="http://localhost/cgi-bin/gb2/gbrowse/".10190714;
echo "<br><iframe src =".$url." width="1000" height="700" >
</iframe>";}
?>
but when I point my browser to
http://localhost/cgi-bin/gb2/gbrowse/10190714
I get the attached snapshot

Hi
/usr/lib/cgi-bin/gb2/gbrowse:55
yes I added the entry to /etc/gbrowse/GBrowse.conf

Post by Scott Cain
Hi Umay,
I'm glad you've gotten it working.
What you're describing with asking for one configuration and getting

another

Post by Scott Cain
is what happens when there is a problem with the configuration that you
want. I don't see anything obvious with the configuration you pasted

into

Post by Scott Cain
the email, but my eyes aren't as good a configuration parser as

GBrowse. A

Post by Scott Cain
Do you see anything in the apache error log that indicates that there

is a

Post by Scott Cain
problem?
Did you add an entry for the new configuration file to
/etc/gbrowse/GBrowse.conf?
Scott

'/var/www/html/gbrowse2/databases/1/1/4/114635370/'

Post by umay kulsum
plugins = BatchDumper FastaDumper
gbrowse root = gbrowse
stylesheet = gbrowse.css
buttons = images/buttons
js = js
tmpimages = tmp
region segment = 500
initial landmark = 114635370
balloon tips = 1
drag and drop = 1
cache time = 1
link = AUTO
image widths = 450 640 800 1024
hilite fill = beige
hilite outline = red
default width = 800
default features = 114635370
max segment = 500
default segment = 50
zoom levels = 50 100 200 1000 2000 5000 10000 20000 40000 100000
200000 500000 1000000
show sources = 1
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
examples = 114635370
automatic classes = 114635370
[protein]
feature = protein
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 1
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See protein
details</a></th></tr>
<tr align='left'><th><a
href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
NCBI</a></th></tr>
</table>
key = protein
[pattern]
feature = pattern
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 1
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See gene
details</a></th></tr>
<tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
<tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
</table>
key = pattern
[profile]
feature = profile
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 0
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
<tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
</table>
key = profile

Hi
when I do
git clone https://github.com/GMOD/GBrowse.git
Cloning into 'GBrowse'...
gnutls_handshake() failed: A TLS packet with unexpected length was
received.

Post by Scott Cain
Hi Umay,
I suspect you are using Ubuntu 14.04 (you may have already told me
that--I
don't remember). While working recently on some minor bug fixes

for

Post by Scott Cain
GBrowse, we discovered that when Ubuntu 14.04 was released, they
dramatically rearranged the file structure for system files, which broke
the
GBrowse installer. The easiest way to install GBrowse correctly

Post by Scott Cain
the
moment is to get a GitHub checkout of the current source and

install

Post by Scott Cain
that
git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install
After doing that you should be able to go to
http://localhost/gbrowse2
though the links for sample data sets are written assuming you

have

Post by Scott Cain
fastcgi
installed (which is a good idea to use, because it makes things faster),
but
if you don't have fastcgi, you should still be able to go to
http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample

dataset.

Post by Scott Cain
If
that
works, you should be able to proceed with the tutorial as well.
On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum <

Post by umay kulsum
whenever we write localhost it looks for files in /var/www/html
so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www
On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum

Post by umay kulsum
[Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766]
Command line: '/usr/sbin/apache2'
This is the last comment in /var/log/apache2/error.log...... it
shows
nothing regarding the files not found
127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
/cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain <

Post by Scott Cain
Hi Umay,
What does it say in the apache error log? If you're getting a
message
about a file not being found, it will record where it was

looking

Post by Scott Cain
for the
file. The error log is in /var/log/apache2. The most recent
message
is at
the end of the file.
Scott
Sent from my iPhone

On Sep 17, 2014, at 11:03 PM, umay kulsum
hi
I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast

also but

again
its the same the requested url is not found on the server...
what should I do??
where am I going wrong??
can you please tell me how can I start from scratch that is
uninstall
and then reinstall....

linked to

from
http://localhost/gbrowse2/
I don't know why you have two yeast_chr1+2 directories, but
only
one
of them
will work. The typical configuration would be for the one

/var/lib/gbrowse2/databases to work.
The cgi-bin directory is not in the /var/www directory when
apache
is
typically configured for ubuntu; it's in /usr/lib/cgi-bin,

it
is
in your
case.
Scott

On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
I have installed GBrowse using the command in ubuntu 14.04
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
etc/gbrowse2/GBrowse.conf
var/www/gbrowse2/databases where I have the yeast_chr1+2
folder
with
my own data files
usr/lib/cgi-bin/gb2
var/lib/gbrowse2/databases/yeast_chr1+2 with other files
but still the url http://localhost/cgi-bin/gbrowse2/yeast
shows
the
following url was not found on the server
where is the cgi-bin mentioned in the url located when it

not
in
/var/www/
On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum

Hi
I have installed GBrowse using the command in ubuntu 14.04
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
but when I point my browser to
http://localhost/cgi-bin/gbrowse2/yeast, it shows the
following
url
is
not found on this server..
where is the cgi-bin mentioned in the url located when it

not
in
/var/www/

On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
Hi Umay,
Can you please tell us what you done and where you think

the

process
has failed? For instance, what do you see when you go to
the
built in
sample yeast data set?
Scott
Sent from my iPhone

On Sep 11, 2014, at 11:41 PM, umay kulsum
I have been trying to install and invoke GBrowse since a
month
but to
no result....
can someone help me regarding the installation process.

------------------------------------------------------------------------------

Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.

http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk

_______________________________________________
Gmod-gbrowse mailing list

https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

------------------------------------------------------------------------

Scott Cain, Ph. D. scott

scottcain dot
net
GMOD Coordinator (http://gmod.org/)
216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------

Post by Scott Cain
Scott Cain, Ph. D. scott at scottcain
dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Post by Scott Cain
Ontario Institute for Cancer Research

------------------------------------------------------------------------

Post by Scott Cain
Scott Cain, Ph. D. scott at

scottcain

Post by Scott Cain
dot
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain

dot

Post by Scott Cain
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

Scott Cain

2014-09-26 13:19:34 UTC

Hi Umay,

The chown command changed the GFF file from text to binary? It's not often
I say things are impossible, but that's pretty close. How do you know it
changed it to binary? Are you sure it's binary now?

As for the screenshot you included, it shows that there are still problems
with your configuration: I suspect that gbrowse still can't find various
files it needs to work correctly, like css and javascript files. Please
look at your apache access log for 404 errors to see where it is looking
for files and try to figure out why it's looking in the wrong place.

Scott

Hi Scott
I have done as you directed. The error message is no more there but
not getting the tracks.
screenshot is attached.
and the gff3 file is not being displayed when I open
/var/lib/gbrowse2/databases.
the gff3 file is also attached.
The command chown -R www-data:www-data changes the gff3 file from
plain text to binary
The original gff3 is also attached

Hi Scott,
I have done as you directed. The error message is no more there but
not getting the tracks.
screenshot is attached.

Post by Scott Cain
Hi Umay,
That message at the top of the screenshot you sent is the full error
message. The first line of it has the source of the problem. It

can't open

Post by Scott Cain
the file at /var/lib/gbrowse2/databases/1...... Does that directory

exist

Post by Scott Cain
and does the webserver have permission to open it? Probably the best

thing

Post by Scott Cain
to do is to change ownership of that directory to the user that runs

the

Post by Scott Cain
sudo chown -R www-data:www-data /var/lib/gbrowse2/databases/*
If you're making frequent edits in the databases directories (like when
you're doing the tutorial), you can just make the directory you're

working

Post by Scott Cain
on world writeable, so that the webserver and you can both write files

Post by Scott Cain
the directory without sudo. Of course, this is considerably less
sudo chmod -R a+w /var/lib/gbrowse2/databases/nameofdatabase
Scott

Hi
/usr/lib/cgi-bin/gb2/gbrowse:55
yes I added the entry to /etc/gbrowse/GBrowse.conf

Post by Scott Cain
Hi Umay,
I'm glad you've gotten it working.
What you're describing with asking for one configuration and

getting

Post by Scott Cain
another
is what happens when there is a problem with the configuration

that you

Post by Scott Cain
want. I don't see anything obvious with the configuration you

pasted

Post by Scott Cain
into
the email, but my eyes aren't as good a configuration parser as GBrowse. A
Do you see anything in the apache error log that indicates that

there

Post by Scott Cain
is a
problem?
Did you add an entry for the new configuration file to
/etc/gbrowse/GBrowse.conf?
Scott
On Mon, Sep 22, 2014 at 11:35 PM, umay kulsum <

result of

Post by umay kulsum
yeast but not my own file
why is it so and what can I do for that??
[GENERAL]
description = motifs of 114635370protein
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir
'/var/www/html/gbrowse2/databases/1/1/4/114635370/'
plugins = BatchDumper FastaDumper
gbrowse root = gbrowse
stylesheet = gbrowse.css
buttons = images/buttons
js = js
tmpimages = tmp
region segment = 500
initial landmark = 114635370
balloon tips = 1
drag and drop = 1
cache time = 1
link = AUTO
image widths = 450 640 800 1024
hilite fill = beige
hilite outline = red
default width = 800
default features = 114635370
max segment = 500
default segment = 50
zoom levels = 50 100 200 1000 2000 5000 10000 20000 40000

100000

Post by umay kulsum
200000 500000 1000000
show sources = 1
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
examples = 114635370
automatic classes = 114635370
[protein]
feature = protein
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 1
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See protein
details</a></th></tr>
<tr align='left'><th><a
href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
NCBI</a></th></tr>
</table>
key = protein
[pattern]
feature = pattern
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 1
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See gene
details</a></th></tr>
<tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
<tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about

</a></th></tr>

Post by umay kulsum
</table>
key = pattern
[profile]
feature = profile
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 0
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
<tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about

</a></th></tr>

Post by umay kulsum
</table>
key = profile

Post by Scott Cain
Hi Umay,
I don't really know what the problem is--my guess is that there

is a

Post by Scott Cain
network
problem. Can you try from a different network? Can you clone

other

Post by Scott Cain
things
from git but just not GBrowse (I would find that pretty strange

Post by Scott Cain
it
were
the case)? Also, in case there is a problem with any of the software
packages you are using, you should probably run
sudo apt-get update
sudo apt-get upgrade
to make sure your system is up to date.
Scott
On Mon, Sep 22, 2014 at 4:17 AM, umay kulsum <

Hi
when I do
git clone https://github.com/GMOD/GBrowse.git
Cloning into 'GBrowse'...
fatal: unable to access 'https://github.com/GMOD/GBrowse.git/
gnutls_handshake() failed: A TLS packet with unexpected length

was

received.
On Thu, Sep 18, 2014 at 7:37 PM, Scott Cain <

Post by Scott Cain
Hi Umay,
I suspect you are using Ubuntu 14.04 (you may have already

told

Post by Scott Cain
me
that--I
don't remember). While working recently on some minor bug

fixes

Post by Scott Cain
for
GBrowse, we discovered that when Ubuntu 14.04 was released,

they

Post by Scott Cain
dramatically rearranged the file structure for system files,
which
broke
the
GBrowse installer. The easiest way to install GBrowse

correctly

Post by Scott Cain
at
the
moment is to get a GitHub checkout of the current source and
install
that
git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install
After doing that you should be able to go to
http://localhost/gbrowse2
though the links for sample data sets are written assuming

you

Post by Scott Cain
have
fastcgi
installed (which is a good idea to use, because it makes

things

Post by Scott Cain
faster),
but
if you don't have fastcgi, you should still be able to go to
http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample
dataset.
If
that
works, you should be able to proceed with the tutorial as

well.

Post by Scott Cain
On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum

Post by umay kulsum
whenever we write localhost it looks for files in

/var/www/html

Post by umay kulsum
so I think its looking for /cgi-bin/gb2/gbrowse/yeast in
/var/www
On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum

Post by umay kulsum
[Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid

10766]

Post by umay kulsum
Command line: '/usr/sbin/apache2'
This is the last comment in

/var/log/apache2/error.log......

Post by umay kulsum
it
shows
nothing regarding the files not found
127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
/cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-"

"Mozilla/5.0

Post by umay kulsum
(X11;
Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101

Firefox/28.0"

Post by umay kulsum
On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain

Post by Scott Cain
Hi Umay,
What does it say in the apache error log? If you're

getting

Post by Scott Cain
a
message
about a file not being found, it will record where it was
looking
for the
file. The error log is in /var/log/apache2. The most

recent

Post by Scott Cain
message
is at
the end of the file.
Scott
Sent from my iPhone

On Sep 17, 2014, at 11:03 PM, umay kulsum
hi
I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast

also

but
again
its the same the requested url is not found on the

server...

what should I do??
where am I going wrong??
can you please tell me how can I start from scratch

that is

uninstall
and then reinstall....

On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain
Umay,
Please "reply-all" so that your replies stay on the

GBrowse

mailing
list.
The url you are using is not correct; it should be
http://localhost/cgi-bin/gb2/gbrowse/yeast. This is

linked

to
from
http://localhost/gbrowse2/
I don't know why you have two yeast_chr1+2

directories, but

only
one
of them
will work. The typical configuration would be for the

one

in
/var/lib/gbrowse2/databases to work.
The cgi-bin directory is not in the /var/www directory

when

apache
is
typically configured for ubuntu; it's in

/usr/lib/cgi-bin,

as
it
is
in your
case.
Scott

On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
I have installed GBrowse using the command in ubuntu

14.04

sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
etc/gbrowse2/GBrowse.conf
var/www/gbrowse2/databases where I have the

yeast_chr1+2

folder
with
my own data files
usr/lib/cgi-bin/gb2
var/lib/gbrowse2/databases/yeast_chr1+2 with other

files

but still the url

http://localhost/cgi-bin/gbrowse2/yeast

shows
the
following url was not found on the server
where is the cgi-bin mentioned in the url located

when it

is
not
in
/var/www/
On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum

Hi
I have installed GBrowse using the command in ubuntu
14.04
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
but when I point my browser to
http://localhost/cgi-bin/gbrowse2/yeast, it shows

the

following
url
is
not found on this server..
where is the cgi-bin mentioned in the url located

when it

is
not
in
/var/www/

On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
Hi Umay,
Can you please tell us what you done and where you

think

the
process
has failed? For instance, what do you see when you

to
the
built in
sample yeast data set?
Scott
Sent from my iPhone

On Sep 11, 2014, at 11:41 PM, umay kulsum
I have been trying to install and invoke GBrowse

since

a
month
but to
no result....
can someone help me regarding the installation

process.
------------------------------------------------------------------------------

Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.

http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk

_______________________________________________
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

------------------------------------------------------------------------

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

------------------------------------------------------------------------

Post by Scott Cain
Scott Cain, Ph. D. scott at
scottcain
dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Post by Scott Cain
Ontario Institute for Cancer Research

------------------------------------------------------------------------

Post by Scott Cain
Scott Cain, Ph. D. scott at

scottcain

Post by Scott Cain
dot
net
GMOD Coordinator (http://gmod.org/)

216-392-3087

Post by Scott Cain
Ontario Institute for Cancer Research

------------------------------------------------------------------------

Post by Scott Cain
Scott Cain, Ph. D. scott at

scottcain dot

Post by Scott Cain
net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

umay kulsum

2014-09-26 03:05:19 UTC

Hi Scott,

I have done as you directed. The error message is no more there but
not getting the tracks.
screenshot is attached.

Post by Scott Cain
Hi Umay,
That message at the top of the screenshot you sent is the full error
message. The first line of it has the source of the problem. It can't open
the file at /var/lib/gbrowse2/databases/1...... Does that directory exist
and does the webserver have permission to open it? Probably the best thing
to do is to change ownership of that directory to the user that runs the
sudo chown -R www-data:www-data /var/lib/gbrowse2/databases/*
If you're making frequent edits in the databases directories (like when
you're doing the tutorial), you can just make the directory you're working
on world writeable, so that the webserver and you can both write files in
sudo chmod -R a+w /var/lib/gbrowse2/databases/nameofdatabase
Scott

Hi
/usr/lib/cgi-bin/gb2/gbrowse:55
yes I added the entry to /etc/gbrowse/GBrowse.conf

Post by Scott Cain
Hi Umay,
I'm glad you've gotten it working.
What you're describing with asking for one configuration and getting another
is what happens when there is a problem with the configuration that you
want. I don't see anything obvious with the configuration you pasted into
the email, but my eyes aren't as good a configuration parser as GBrowse. A
Do you see anything in the apache error log that indicates that there is a
problem?
Did you add an entry for the new configuration file to
/etc/gbrowse/GBrowse.conf?
Scott

Post by umay kulsum
Hi
Thank you scott....got GBrowse installed with git clone...
example database of yeast is also working properly...
but now I have created my own conf file as 114635370.conf in
etc/gbrowse2/gbrowse.conf folder but when I run
http://localhost/cgi-bin/gb2/gbrowse/114635370 it gives the result of
yeast but not my own file
why is it so and what can I do for that??
[GENERAL]
description = motifs of 114635370protein
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir
'/var/www/html/gbrowse2/databases/1/1/4/114635370/'
plugins = BatchDumper FastaDumper
gbrowse root = gbrowse
stylesheet = gbrowse.css
buttons = images/buttons
js = js
tmpimages = tmp
region segment = 500
initial landmark = 114635370
balloon tips = 1
drag and drop = 1
cache time = 1
link = AUTO
image widths = 450 640 800 1024
hilite fill = beige
hilite outline = red
default width = 800
default features = 114635370
max segment = 500
default segment = 50
zoom levels = 50 100 200 1000 2000 5000 10000 20000 40000 100000
200000 500000 1000000
show sources = 1
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
examples = 114635370
automatic classes = 114635370
[protein]
feature = protein
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 1
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See protein
details</a></th></tr>
<tr align='left'><th><a
href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
NCBI</a></th></tr>
</table>
key = protein
[pattern]
feature = pattern
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 1
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See gene
details</a></th></tr>
<tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
<tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
</table>
key = pattern
[profile]
feature = profile
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 0
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
<tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
</table>
key = profile

Post by Scott Cain
Hi Umay,
I don't really know what the problem is--my guess is that there is a network
problem. Can you try from a different network? Can you clone other things
from git but just not GBrowse (I would find that pretty strange if it
were
the case)? Also, in case there is a problem with any of the software
packages you are using, you should probably run
sudo apt-get update
sudo apt-get upgrade
to make sure your system is up to date.
Scott

Hi
when I do
git clone https://github.com/GMOD/GBrowse.git
Cloning into 'GBrowse'...
gnutls_handshake() failed: A TLS packet with unexpected length was
received.

Post by Scott Cain
Hi Umay,
I suspect you are using Ubuntu 14.04 (you may have already told me
that--I
don't remember). While working recently on some minor bug fixes for
GBrowse, we discovered that when Ubuntu 14.04 was released, they
dramatically rearranged the file structure for system files, which
broke
the
GBrowse installer. The easiest way to install GBrowse correctly at
the
moment is to get a GitHub checkout of the current source and
install
that
git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install
After doing that you should be able to go to
http://localhost/gbrowse2
though the links for sample data sets are written assuming you have
fastcgi
installed (which is a good idea to use, because it makes things
faster),
but
if you don't have fastcgi, you should still be able to go to
http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.
If
that
works, you should be able to proceed with the tutorial as well.
On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum

Post by umay kulsum
whenever we write localhost it looks for files in /var/www/html
so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www
On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum

Post by umay kulsum
[Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766]
Command line: '/usr/sbin/apache2'
This is the last comment in /var/log/apache2/error.log...... it
shows
nothing regarding the files not found
127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
/cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0
(X11;
Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain

Post by Scott Cain
Hi Umay,
What does it say in the apache error log? If you're getting a
message
about a file not being found, it will record where it was
looking
for the
file. The error log is in /var/log/apache2. The most recent
message
is at
the end of the file.
Scott
Sent from my iPhone

On Sep 17, 2014, at 11:03 PM, umay kulsum
hi
I have tried http://localhost/cgi-bin/gb2/gbrowse/yeast also
but
again
its the same the requested url is not found on the server...
what should I do??
where am I going wrong??
can you please tell me how can I start from scratch that is
uninstall
and then reinstall....

On Wed, Sep 17, 2014 at 7:47 PM, Scott Cain
Umay,
Please "reply-all" so that your replies stay on the GBrowse
mailing
list.
The url you are using is not correct; it should be
http://localhost/cgi-bin/gb2/gbrowse/yeast. This is linked
to
from
http://localhost/gbrowse2/
I don't know why you have two yeast_chr1+2 directories, but
only
one
of them
will work. The typical configuration would be for the one
in
/var/lib/gbrowse2/databases to work.
The cgi-bin directory is not in the /var/www directory when
apache
is
typically configured for ubuntu; it's in /usr/lib/cgi-bin,
as
it
is
in your
case.
Scott

On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
I have installed GBrowse using the command in ubuntu 14.04
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
etc/gbrowse2/GBrowse.conf
var/www/gbrowse2/databases where I have the yeast_chr1+2
folder
with
my own data files
usr/lib/cgi-bin/gb2
var/lib/gbrowse2/databases/yeast_chr1+2 with other files
but still the url http://localhost/cgi-bin/gbrowse2/yeast
shows
the
following url was not found on the server
where is the cgi-bin mentioned in the url located when it
is
not
in
/var/www/
On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum

Hi
I have installed GBrowse using the command in ubuntu
14.04
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
but when I point my browser to
http://localhost/cgi-bin/gbrowse2/yeast, it shows the
following
url
is
not found on this server..
where is the cgi-bin mentioned in the url located when it
is
not
in
/var/www/

On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
Hi Umay,
Can you please tell us what you done and where you think
the
process
has failed? For instance, what do you see when you go
to
the
built in
sample yeast data set?
Scott
Sent from my iPhone

On Sep 11, 2014, at 11:41 PM, umay kulsum
I have been trying to install and invoke GBrowse since
a
month
but to
no result....
can someone help me regarding the installation process.
------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
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, Ph. D. scott at scottcain
dot
net
GMOD Coordinator (http://gmod.org/)
216-392-3087
Ontario Institute for Cancer Research

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

umay kulsum

2014-09-26 03:47:24 UTC

Hi Scott,
I have done as you directed. The error message is no more there but
not getting the tracks.
screenshot is attached.

Hi
/usr/lib/cgi-bin/gb2/gbrowse:55
yes I added the entry to /etc/gbrowse/GBrowse.conf

Post by umay kulsum
Hi
Thank you scott....got GBrowse installed with git clone...
example database of yeast is also working properly...
but now I have created my own conf file as 114635370.conf in
etc/gbrowse2/gbrowse.conf folder but when I run
http://localhost/cgi-bin/gb2/gbrowse/114635370 it gives the result of
yeast but not my own file
why is it so and what can I do for that??
[GENERAL]
description = motifs of 114635370protein
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor memory
-dir
'/var/www/html/gbrowse2/databases/1/1/4/114635370/'
plugins = BatchDumper FastaDumper
gbrowse root = gbrowse
stylesheet = gbrowse.css
buttons = images/buttons
js = js
tmpimages = tmp
region segment = 500
initial landmark = 114635370
balloon tips = 1
drag and drop = 1
cache time = 1
link = AUTO
image widths = 450 640 800 1024
hilite fill = beige
hilite outline = red
default width = 800
default features = 114635370
max segment = 500
default segment = 50
zoom levels = 50 100 200 1000 2000 5000 10000 20000 40000 100000
200000 500000 1000000
show sources = 1
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor = beige
examples = 114635370
automatic classes = 114635370
[protein]
feature = protein
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 1
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See protein
details</a></th></tr>
<tr align='left'><th><a
href="http://www.ncbi.nlm.nih.gov/protein/114635370">Go to
NCBI</a></th></tr>
</table>
key = protein
[pattern]
feature = pattern
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 1
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="/cgi-bin/gbrowse_details/motif?name=">See gene
details</a></th></tr>
<tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
<tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
</table>
key = pattern
[profile]
feature = profile
glyph = so_transcript
bgcolor = yellow
forwardcolor = yellow
reversecolor = turquoise
height = 6
description = 0
balloon hover width = 350
balloon hover = sub { my = shift; return join ' ',->notes }
balloon click width = 450
balloon click = <table>
<tr><th rowspan="5" align="left"><br>
This protein brought to you by <a
href="http://www.expasy.ch">EXPASY</a>.</th>
<th bgcolor="cyan">Gene </th>
</tr>
<tr align='left'><th><a
href="http://en.wikipedia.org/wiki/Special:Search?search=">Ask
Wikipedia about </a></th></tr>
<tr align='left'><th><a
href="http://www.google.com/search?q=">Ask Google about </a></th></tr>
</table>
key = profile

Post by Scott Cain
Hi Umay,
I don't really know what the problem is--my guess is that there is a
network
problem. Can you try from a different network? Can you clone other things
from git but just not GBrowse (I would find that pretty strange if it
were
the case)? Also, in case there is a problem with any of the software
packages you are using, you should probably run
sudo apt-get update
sudo apt-get upgrade
to make sure your system is up to date.
Scott

Hi
when I do
git clone https://github.com/GMOD/GBrowse.git
Cloning into 'GBrowse'...
gnutls_handshake() failed: A TLS packet with unexpected length was
received.

Post by Scott Cain
Hi Umay,
I suspect you are using Ubuntu 14.04 (you may have already told me
that--I
don't remember). While working recently on some minor bug fixes for
GBrowse, we discovered that when Ubuntu 14.04 was released, they
dramatically rearranged the file structure for system files, which
broke
the
GBrowse installer. The easiest way to install GBrowse correctly at
the
moment is to get a GitHub checkout of the current source and
install
that
git clone https://github.com/GMOD/GBrowse.git
cd GBrowse
perl Build.PL #accepting the defaults should be fine
./Build
./Build test
sudo ./Build install
After doing that you should be able to go to
http://localhost/gbrowse2
though the links for sample data sets are written assuming you have
fastcgi
installed (which is a good idea to use, because it makes things
faster),
but
if you don't have fastcgi, you should still be able to go to
http://localhost/cgi-bin/gb2/gbrowse/yeast to see a sample dataset.
If
that
works, you should be able to proceed with the tutorial as well.
On Thu, Sep 18, 2014 at 2:15 AM, umay kulsum

Post by umay kulsum
whenever we write localhost it looks for files in /var/www/html
so I think its looking for /cgi-bin/gb2/gbrowse/yeast in /var/www
On Thu, Sep 18, 2014 at 11:25 AM, umay kulsum

Post by umay kulsum
[Thu Sep 18 09:03:14.584273 2014] [core:notice] [pid 10766]
Command line: '/usr/sbin/apache2'
This is the last comment in /var/log/apache2/error.log...... it
shows
nothing regarding the files not found
127.0.0.1 - - [18/Sep/2014:11:13:58 +0530] "GET
/cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513 "-" "Mozilla/5.0
(X11;
Ubuntu; Linux x86_64; rv:28.0) Gecko/20100101 Firefox/28.0"
On Thu, Sep 18, 2014 at 10:34 AM, Scott Cain

Post by Scott Cain
Hi Umay,
What does it say in the apache error log? If you're getting
a
message
about a file not being found, it will record where it was
looking
for the
file. The error log is in /var/log/apache2. The most recent
message
is at
the end of the file.
Scott
Sent from my iPhone

On Wed, Sep 17, 2014 at 4:15 AM, umay kulsum
I have installed GBrowse using the command in ubuntu 14.04
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
etc/gbrowse2/GBrowse.conf
var/www/gbrowse2/databases where I have the yeast_chr1+2
folder
with
my own data files
usr/lib/cgi-bin/gb2
var/lib/gbrowse2/databases/yeast_chr1+2 with other files
but still the url http://localhost/cgi-bin/gbrowse2/yeast
shows
the
following url was not found on the server
where is the cgi-bin mentioned in the url located when it
is
not
in
/var/www/
On Wed, Sep 17, 2014 at 8:54 AM, umay kulsum

Hi
I have installed GBrowse using the command in ubuntu
14.04
sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
but when I point my browser to
http://localhost/cgi-bin/gbrowse2/yeast, it shows the
following
url
is
not found on this server..
where is the cgi-bin mentioned in the url located when it
is
not
in
/var/www/

On Tue, Sep 16, 2014 at 2:28 AM, Scott Cain
Hi Umay,
Can you please tell us what you done and where you think
the
process
has failed? For instance, what do you see when you go
to
the
built in
sample yeast data set?
Scott
Sent from my iPhone

On Sep 11, 2014, at 11:41 PM, umay kulsum
I have been trying to install and invoke GBrowse since
a
month
but to
no result....
can someone help me regarding the installation process.
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--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott
at
scottcain dot
net
GMOD Coordinator (http://gmod.org/)
216-392-3087
Ontario Institute for Cancer Research

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

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

umay kulsum

2014-09-26 04:22:49 UTC