[Gmod-gbrowse] Need a help

Discussion:

Scott Cain

2014-11-26 16:23:28 UTC

Hi Swetha,

The only way I can think of to do that is with separate configuration files
for GBrowse unfortunately. The "data source" drop down was originally
conceived of to allow selecting different "species", but that concept
doesn't map very well to strains of a virus. There are two approaches I
could see using:

1. Revamp the way you're using GBrowse data sources altogether, so that
each data source represents one type of virus, so in the drop down you'd
have two entries, one for H. influenzae and one for the other virus. Each
strain would then be analogous a chromosome. One advantage to this
approach is that when/if you have hundreds of strains of a virus the drop
down will still be useable (that is, a drop down menu with a more than
20-30 entries is very unwieldy). Users would be able to use the search box
to find strains they are interested in. A potential downside is that
searching for a particular gene would yield results for that gene in every
strain.

2. Create separate gbrowse2 config directories for each virus. Then you
need to edit gbrowse2.conf file that lives in the apache configuration;
where that is varies depending on your OS; on Ubuntu 12.04 it's in
/etc/apache2/conf.d/. You'll need separate cgi-bin directories too, for
example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and
/usr/lib/cgi-bin/Segb2 for the Something else virus :-) In the apache
gbrowse.conf file you need separate entries for the different cgi-bin
directores that have different "SetEnv GBROWSE_CONF" entries to point at
the separate gbrowse config directories.

Obviously, it's up to you to decide which is better; there will be work
either way. I suggest that if you choose the second path that you make
very incremental changes and test that GBrowse still works all along the
way, because there are several moving parts that could break GBrowse and
with the changes required, it might be difficult to sort out what happened
if something goes wrong.

Scott

Respected Sir,
We have developed a database for Haemophilus influenzae and we used
Gbrowse to visualize their annotation. Now, we are developing the database
for other organism and we need to use the Gbrowse. We are going to host the
second database in the same server where GBrowse is already installed. But,
I have a doubt. The dropdown menu for the second database should be changed
in GBrowse. How is it possible?
In Haemophilus influenzae database, we have included 10 different strains
of H. influenzae. I have attached the screenshot for your reference.
In second database, I need to include 25 strains of other organism.
Query: these 25 strains should be in dropdown menu instead of those 10
strains. And, When the user access H. influenzae database, 10 strains
should be there and when the user access second database, 25 strains should
be there. How is it possible?
Waiting for your reply.
Yours sincerely,
Swetha R G.

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

Scott Cain

2015-03-04 14:14:30 UTC

Permalink

Hi Swetha,

Please always ask questions on the mailing list (cc'ed here).

If you are using fastcgi, you may need to restart apache to recognize the
change you made in your config file. The other possibility is that you
didn't really edit the config file that GBrowse is using (believe me, I've
done that many times, where I edit a copy of the config file and can't
understand why it isn't having any effect).

Scott

Dear Sir,
I have a doubt in Gbrowse. Can you please help me sir?
Herewith, I have attached the conf file.
It works well in Browser. In file, suppose, If I change initial landmark =
NC_022659.1:1..10000 to *initial landmark = NC_022659.1:20639..15623*,
the browser displays the old landmark itself (i.e 1..10000). I know its
because of some cache problem. If I delete the browser history, then the
browser displays the new landmark. Can you please solve this issue?
Yours sincerely,
Swetha R G,
Senior Research Fellow (ICMR),
VIT University,
Vellore,
India.
On Thu, Nov 27, 2014 at 8:21 PM, Rayapadi Swetha <

Dear Sir,
Tons of thanks. I followed your suggestion, option 2. Now it works well.
You helped me a lot in GBrowse (Starting from installation to till now).
Thank you so much. I used GBrowse in two databases and both are published.
One in Genomics and other in Computers in Biology and Medicine. This
publication is not possible without your guidance.
Thank you.
Yours sincerely,
Swetha R G,
Research Associate,
School of BioSciences and Technology,
VIT University,
India.
On Thu, Nov 27, 2014 at 9:27 AM, Rayapadi Swetha <

Dear Sir,
Thank you so much for your quick reply. Let me work according to your
suggestion and If I stuck at any point, Please help me.
Yours sincerely,
Swetha R G.

Post by Scott Cain
Hi Swetha,
The only way I can think of to do that is with separate configuration
files for GBrowse unfortunately. The "data source" drop down was
originally conceived of to allow selecting different "species", but that
concept doesn't map very well to strains of a virus. There are two
1. Revamp the way you're using GBrowse data sources altogether, so that
each data source represents one type of virus, so in the drop down you'd
have two entries, one for H. influenzae and one for the other virus.
Each strain would then be analogous a chromosome. One advantage to
this approach is that when/if you have hundreds of strains of a virus the
drop down will still be useable (that is, a drop down menu with a more than
20-30 entries is very unwieldy). Users would be able to use the search box
to find strains they are interested in. A potential downside is that
searching for a particular gene would yield results for that gene in every
strain.
2. Create separate gbrowse2 config directories for each virus. Then
you need to edit gbrowse2.conf file that lives in the apache configuration;
where that is varies depending on your OS; on Ubuntu 12.04 it's in
/etc/apache2/conf.d/. You'll need separate cgi-bin directories too, for
example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and
/usr/lib/cgi-bin/Segb2 for the Something else virus :-) In the apache
gbrowse.conf file you need separate entries for the different cgi-bin
directores that have different "SetEnv GBROWSE_CONF" entries to point at
the separate gbrowse config directories.
Obviously, it's up to you to decide which is better; there will be work
either way. I suggest that if you choose the second path that you make
very incremental changes and test that GBrowse still works all
along the way, because there are several moving parts that could break
GBrowse and with the changes required, it might be difficult to sort out
what happened if something goes wrong.
Scott
On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <

Respected Sir,
We have developed a database for Haemophilus influenzae and we used
Gbrowse to visualize their annotation. Now, we are developing the database
for other organism and we need to use the Gbrowse. We are going to host the
second database in the same server where GBrowse is already installed. But,
I have a doubt. The dropdown menu for the second database should be changed
in GBrowse. How is it possible?
In Haemophilus influenzae database, we have included 10 different
strains of H. influenzae. I have attached the screenshot for your reference.
In second database, I need to include 25 strains of other organism.
Query: these 25 strains should be in dropdown menu instead of those 10
strains. And, When the user access H. influenzae database, 10 strains
should be there and when the user access second database, 25 strains should
be there. How is it possible?
Waiting for your reply.
Yours sincerely,
Swetha R G.

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

Rayapadi Swetha

2015-03-04 16:15:17 UTC

Permalink

Dear sir,

I edited in the config file where GBrowse is using.

If I delete the browsing history, then its show the new landmark. Is there
any possibility without deleting the browser history? Kindly let me know

Post by Scott Cain
Hi Swetha,
Please always ask questions on the mailing list (cc'ed here).
If you are using fastcgi, you may need to restart apache to recognize the
change you made in your config file. The other possibility is that you
didn't really edit the config file that GBrowse is using (believe me, I've
done that many times, where I edit a copy of the config file and can't
understand why it isn't having any effect).
Scott

Dear Sir,
I have a doubt in Gbrowse. Can you please help me sir?
Herewith, I have attached the conf file.
It works well in Browser. In file, suppose, If I change initial landmark
= NC_022659.1:1..10000 to *initial landmark = NC_022659.1:20639..15623*,
the browser displays the old landmark itself (i.e 1..10000). I know its
because of some cache problem. If I delete the browser history, then the
browser displays the new landmark. Can you please solve this issue?
Yours sincerely,
Swetha R G,
Senior Research Fellow (ICMR),
VIT University,
Vellore,
India.
On Thu, Nov 27, 2014 at 8:21 PM, Rayapadi Swetha <

Dear Sir,
Thank you so much for your quick reply. Let me work according to your
suggestion and If I stuck at any point, Please help me.
Yours sincerely,
Swetha R G.

Post by Scott Cain
Hi Swetha,
The only way I can think of to do that is with separate configuration
files for GBrowse unfortunately. The "data source" drop down was
originally conceived of to allow selecting different "species", but that
concept doesn't map very well to strains of a virus. There are two
1. Revamp the way you're using GBrowse data sources altogether, so
that each data source represents one type of virus, so in the drop down
you'd have two entries, one for H. influenzae and one for the other
virus. Each strain would then be analogous a chromosome. One
advantage to this approach is that when/if you have hundreds of strains of
a virus the drop down will still be useable (that is, a drop down menu with
a more than 20-30 entries is very unwieldy). Users would be able to use
the search box to find strains they are interested in. A potential
downside is that searching for a particular gene would yield results for
that gene in every strain.
2. Create separate gbrowse2 config directories for each virus. Then
you need to edit gbrowse2.conf file that lives in the apache configuration;
where that is varies depending on your OS; on Ubuntu 12.04 it's in
/etc/apache2/conf.d/. You'll need separate cgi-bin directories too, for
example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and
/usr/lib/cgi-bin/Segb2 for the Something else virus :-) In the apache
gbrowse.conf file you need separate entries for the different cgi-bin
directores that have different "SetEnv GBROWSE_CONF" entries to point at
the separate gbrowse config directories.
Obviously, it's up to you to decide which is better; there will be
work either way. I suggest that if you choose the second path that you
make very incremental changes and test that GBrowse still works all
along the way, because there are several moving parts that could break
GBrowse and with the changes required, it might be difficult to sort out
what happened if something goes wrong.
Scott
On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <

Respected Sir,
We have developed a database for Haemophilus influenzae and we used
Gbrowse to visualize their annotation. Now, we are developing the database
for other organism and we need to use the Gbrowse. We are going to host the
second database in the same server where GBrowse is already installed. But,
I have a doubt. The dropdown menu for the second database should be changed
in GBrowse. How is it possible?
In Haemophilus influenzae database, we have included 10 different
strains of H. influenzae. I have attached the screenshot for your reference.
In second database, I need to include 25 strains of other organism.
Query: these 25 strains should be in dropdown menu instead of those
10 strains. And, When the user access H. influenzae database, 10 strains
should be there and when the user access second database, 25 strains should
be there. How is it possible?
Waiting for your reply.
Yours sincerely,
Swetha R G.

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

2015-03-04 19:18:01 UTC

Permalink

Hi Swetha,

I assume you mean you delete the browser's cache and then the changes show
up, right? There is not much GBrowse can do to force a browser to refresh
its cache, but it generally happens on its own in a relatively short period
of time. I would guess that your users won't even notice.

Scott

Post by Rayapadi Swetha
Dear sir,
I edited in the config file where GBrowse is using.
If I delete the browsing history, then its show the new landmark. Is there
any possibility without deleting the browser history? Kindly let me know

Dear Sir,
I have a doubt in Gbrowse. Can you please help me sir?
Herewith, I have attached the conf file.
It works well in Browser. In file, suppose, If I change initial landmark
= NC_022659.1:1..10000 to *initial landmark = NC_022659.1:20639..15623*,
the browser displays the old landmark itself (i.e 1..10000). I know its
because of some cache problem. If I delete the browser history, then the
browser displays the new landmark. Can you please solve this issue?
Yours sincerely,
Swetha R G,
Senior Research Fellow (ICMR),
VIT University,
Vellore,
India.
On Thu, Nov 27, 2014 at 8:21 PM, Rayapadi Swetha <

Dear Sir,
Tons of thanks. I followed your suggestion, option 2. Now it works
well. You helped me a lot in GBrowse (Starting from installation to till
now). Thank you so much. I used GBrowse in two databases and both are
published. One in Genomics and other in Computers in Biology and Medicine.
This publication is not possible without your guidance.
Thank you.
Yours sincerely,
Swetha R G,
Research Associate,
School of BioSciences and Technology,
VIT University,
India.
On Thu, Nov 27, 2014 at 9:27 AM, Rayapadi Swetha <

Dear Sir,
Thank you so much for your quick reply. Let me work according to your
suggestion and If I stuck at any point, Please help me.
Yours sincerely,
Swetha R G.

Post by Scott Cain
Hi Swetha,
The only way I can think of to do that is with separate configuration
files for GBrowse unfortunately. The "data source" drop down was
originally conceived of to allow selecting different "species", but that
concept doesn't map very well to strains of a virus. There are two
1. Revamp the way you're using GBrowse data sources altogether, so
that each data source represents one type of virus, so in the drop down
you'd have two entries, one for H. influenzae and one for the other
virus. Each strain would then be analogous a chromosome. One
advantage to this approach is that when/if you have hundreds of strains of
a virus the drop down will still be useable (that is, a drop down menu with
a more than 20-30 entries is very unwieldy). Users would be able to use
the search box to find strains they are interested in. A potential
downside is that searching for a particular gene would yield results for
that gene in every strain.
2. Create separate gbrowse2 config directories for each virus. Then
you need to edit gbrowse2.conf file that lives in the apache configuration;
where that is varies depending on your OS; on Ubuntu 12.04 it's in
/etc/apache2/conf.d/. You'll need separate cgi-bin directories too, for
example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and
/usr/lib/cgi-bin/Segb2 for the Something else virus :-) In the apache
gbrowse.conf file you need separate entries for the different cgi-bin
directores that have different "SetEnv GBROWSE_CONF" entries to point at
the separate gbrowse config directories.
Obviously, it's up to you to decide which is better; there will be
work either way. I suggest that if you choose the second path that you
make very incremental changes and test that GBrowse still works all
along the way, because there are several moving parts that could break
GBrowse and with the changes required, it might be difficult to sort out
what happened if something goes wrong.
Scott
On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <

Respected Sir,
We have developed a database for Haemophilus influenzae and we used
Gbrowse to visualize their annotation. Now, we are developing the database
for other organism and we need to use the Gbrowse. We are going to host the
second database in the same server where GBrowse is already installed. But,
I have a doubt. The dropdown menu for the second database should be changed
in GBrowse. How is it possible?
In Haemophilus influenzae database, we have included 10 different
strains of H. influenzae. I have attached the screenshot for your reference.
In second database, I need to include 25 strains of other organism.
Query: these 25 strains should be in dropdown menu instead of those
10 strains. And, When the user access H. influenzae database, 10 strains
should be there and when the user access second database, 25 strains should
be there. How is it possible?
Waiting for your reply.
Yours sincerely,
Swetha R G.

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

Rayapadi Swetha

2015-03-05 04:31:54 UTC

Permalink

Hi Sir,

Yes, When I delete the browser's cache, it shows up the new initial
landmark.

Whenever, I am changing the initial land mark, I need to delete the
browsers' cache to display the changed initial land mark. How to solve this
issue sir? Is there anything I can change in GBrowse files to resolve this?

Yours sincerely,
Swetha R G.

Post by Scott Cain
Hi Swetha,
I assume you mean you delete the browser's cache and then the changes show
up, right? There is not much GBrowse can do to force a browser to refresh
its cache, but it generally happens on its own in a relatively short period
of time. I would guess that your users won't even notice.
Scott
On Wed, Mar 4, 2015 at 11:15 AM, Rayapadi Swetha <

Post by Rayapadi Swetha
Dear sir,
I edited in the config file where GBrowse is using.
If I delete the browsing history, then its show the new landmark. Is
there any possibility without deleting the browser history? Kindly let me
know

Post by Scott Cain
Hi Swetha,
Please always ask questions on the mailing list (cc'ed here).
If you are using fastcgi, you may need to restart apache to recognize
the change you made in your config file. The other possibility is that you
didn't really edit the config file that GBrowse is using (believe me, I've
done that many times, where I edit a copy of the config file and can't
understand why it isn't having any effect).
Scott
On Wed, Mar 4, 2015 at 6:58 AM, Rayapadi Swetha <

Dear Sir,
I have a doubt in Gbrowse. Can you please help me sir?
Herewith, I have attached the conf file.
It works well in Browser. In file, suppose, If I change initial
landmark = NC_022659.1:1..10000 to *initial landmark =
NC_022659.1:20639..15623*, the browser displays the old landmark
itself (i.e 1..10000). I know its because of some cache problem. If I
delete the browser history, then the browser displays the new landmark. Can
you please solve this issue?
Yours sincerely,
Swetha R G,
Senior Research Fellow (ICMR),
VIT University,
Vellore,
India.
On Thu, Nov 27, 2014 at 8:21 PM, Rayapadi Swetha <

Dear Sir,
Tons of thanks. I followed your suggestion, option 2. Now it works
well. You helped me a lot in GBrowse (Starting from installation to till
now). Thank you so much. I used GBrowse in two databases and both are
published. One in Genomics and other in Computers in Biology and Medicine.
This publication is not possible without your guidance.
Thank you.
Yours sincerely,
Swetha R G,
Research Associate,
School of BioSciences and Technology,
VIT University,
India.
On Thu, Nov 27, 2014 at 9:27 AM, Rayapadi Swetha <

Dear Sir,
Thank you so much for your quick reply. Let me work according to your
suggestion and If I stuck at any point, Please help me.
Yours sincerely,
Swetha R G.

Post by Scott Cain
Hi Swetha,
The only way I can think of to do that is with separate
configuration files for GBrowse unfortunately. The "data source" drop down
was originally conceived of to allow selecting different "species", but
that concept doesn't map very well to strains of a virus. There are two
1. Revamp the way you're using GBrowse data sources altogether, so
that each data source represents one type of virus, so in the drop down
you'd have two entries, one for H. influenzae and one for the other
virus. Each strain would then be analogous a chromosome. One
advantage to this approach is that when/if you have hundreds of strains of
a virus the drop down will still be useable (that is, a drop down menu with
a more than 20-30 entries is very unwieldy). Users would be able to use
the search box to find strains they are interested in. A potential
downside is that searching for a particular gene would yield results for
that gene in every strain.
2. Create separate gbrowse2 config directories for each virus. Then
you need to edit gbrowse2.conf file that lives in the apache configuration;
where that is varies depending on your OS; on Ubuntu 12.04 it's in
/etc/apache2/conf.d/. You'll need separate cgi-bin directories too, for
example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and
/usr/lib/cgi-bin/Segb2 for the Something else virus :-) In the apache
gbrowse.conf file you need separate entries for the different cgi-bin
directores that have different "SetEnv GBROWSE_CONF" entries to point at
the separate gbrowse config directories.
Obviously, it's up to you to decide which is better; there will be
work either way. I suggest that if you choose the second path that you
make very incremental changes and test that GBrowse still works all
along the way, because there are several moving parts that could break
GBrowse and with the changes required, it might be difficult to sort out
what happened if something goes wrong.
Scott
On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <

Respected Sir,
We have developed a database for Haemophilus influenzae and we used
Gbrowse to visualize their annotation. Now, we are developing the database
for other organism and we need to use the Gbrowse. We are going to host the
second database in the same server where GBrowse is already installed. But,
I have a doubt. The dropdown menu for the second database should be changed
in GBrowse. How is it possible?
In Haemophilus influenzae database, we have included 10 different
strains of H. influenzae. I have attached the screenshot for your reference.
In second database, I need to include 25 strains of other organism.
Query: these 25 strains should be in dropdown menu instead of those
10 strains. And, When the user access H. influenzae database, 10 strains
should be there and when the user access second database, 25 strains should
be there. How is it possible?
Waiting for your reply.
Yours sincerely,
Swetha R G.

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

Rayapadi Swetha

2015-03-04 11:59:40 UTC

Permalink

Dear Sir,

Tons of thanks. I followed your suggestion, option 2. Now it works well.
You helped me a lot in GBrowse (Starting from installation to till now).
Thank you so much. I used GBrowse in two databases and both are published.
One in Genomics and other in Computers in Biology and Medicine. This
publication is not possible without your guidance.

Thank you.

Yours sincerely,
Swetha R G,
Research Associate,
School of BioSciences and Technology,
VIT University,
India.

Dear Sir,
Thank you so much for your quick reply. Let me work according to your
suggestion and If I stuck at any point, Please help me.
Yours sincerely,
Swetha R G.

Post by Scott Cain
Hi Swetha,
The only way I can think of to do that is with separate configuration
files for GBrowse unfortunately. The "data source" drop down was
originally conceived of to allow selecting different "species", but that
concept doesn't map very well to strains of a virus. There are two
1. Revamp the way you're using GBrowse data sources altogether, so that
each data source represents one type of virus, so in the drop down you'd
have two entries, one for H. influenzae and one for the other virus.
Each strain would then be analogous a chromosome. One advantage to this
approach is that when/if you have hundreds of strains of a virus the drop
down will still be useable (that is, a drop down menu with a more than
20-30 entries is very unwieldy). Users would be able to use the search box
to find strains they are interested in. A potential downside is that
searching for a particular gene would yield results for that gene in every
strain.
2. Create separate gbrowse2 config directories for each virus. Then you
need to edit gbrowse2.conf file that lives in the apache configuration;
where that is varies depending on your OS; on Ubuntu 12.04 it's in
/etc/apache2/conf.d/. You'll need separate cgi-bin directories too, for
example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and
/usr/lib/cgi-bin/Segb2 for the Something else virus :-) In the apache
gbrowse.conf file you need separate entries for the different cgi-bin
directores that have different "SetEnv GBROWSE_CONF" entries to point at
the separate gbrowse config directories.
Obviously, it's up to you to decide which is better; there will be work
either way. I suggest that if you choose the second path that you make
very incremental changes and test that GBrowse still works all along the
way, because there are several moving parts that could break GBrowse and
with the changes required, it might be difficult to sort out what happened
if something goes wrong.
Scott
On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <

Respected Sir,
We have developed a database for Haemophilus influenzae and we used
Gbrowse to visualize their annotation. Now, we are developing the database
for other organism and we need to use the Gbrowse. We are going to host the
second database in the same server where GBrowse is already installed. But,
I have a doubt. The dropdown menu for the second database should be changed
in GBrowse. How is it possible?
In Haemophilus influenzae database, we have included 10 different
strains of H. influenzae. I have attached the screenshot for your reference.
In second database, I need to include 25 strains of other organism.
Query: these 25 strains should be in dropdown menu instead of those 10
strains. And, When the user access H. influenzae database, 10 strains
should be there and when the user access second database, 25 strains should
be there. How is it possible?
Waiting for your reply.
Yours sincerely,
Swetha R G.

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