selecting data source results in a search result

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selecting data source results in a search result

Kenlee Nakasugi-2
Hi again,

I updated our gbrowse instance with a new database. When I select it from the 'data source' drop down list, the first page it displays is a search result rather than the Overview/Region/Details panes.
Our other versions load correctly.
You can view it here: http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/

I checked the config files and they seem to be ok. I even commented out the 'examples' and 'initial landmark' options, cleared the database cache, reinstalled the database.

I'm not sure why this is happening - the only thing I can think of is that maybe there are non-unique entries in the fasta or gff file and it's having trouble selecting the right one to display. But i checked and they seem ok.

Any advice on what might be causing this?

Thanks,
Ken

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

Kenlee Nakasugi

Rm873, Bldg-G08 (level 8)
School of Molecular Bioscience
University of New South Wales
Ph: 02-9114-1321

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
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Re: selecting data source results in a search result

Scott Cain
Hi Ken,

I suspect you have a cookie that is causing that behavior, because when I go to your link, I get an initial empty page that I would expect (screenshot attached).  Try going to this url to reset the cookies:


Scott



On Fri, Nov 8, 2013 at 2:55 AM, Kenlee Nakasugi <[hidden email]> wrote:
Hi again,

I updated our gbrowse instance with a new database. When I select it from the 'data source' drop down list, the first page it displays is a search result rather than the Overview/Region/Details panes.
Our other versions load correctly.
You can view it here: http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/

I checked the config files and they seem to be ok. I even commented out the 'examples' and 'initial landmark' options, cleared the database cache, reinstalled the database.

I'm not sure why this is happening - the only thing I can think of is that maybe there are non-unique entries in the fasta or gff file and it's having trouble selecting the right one to display. But i checked and they seem ok.

Any advice on what might be causing this?

Thanks,
Ken

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

Kenlee Nakasugi

Rm873, Bldg-G08 (level 8)
School of Molecular Bioscience
University of New South Wales
Ph: 02-9114-1321

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
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Re: selecting data source results in a search result

Kenlee Nakasugi-2
Hi Scott,

Hmm that's weird because I had tried it on multiple computers at home and work looking at that database page for the first time (I had looked at v03 database from these computers previously though).
Anyway reset=1 did the trick. I might include this in all redirects.

Thanks
Ken



From: Scott Cain [[hidden email]]
Sent: Saturday, November 09, 2013 2:17 AM
To: Kenlee Nakasugi
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] selecting data source results in a search result

Hi Ken,

I suspect you have a cookie that is causing that behavior, because when I go to your link, I get an initial empty page that I would expect (screenshot attached).  Try going to this url to reset the cookies:


Scott



On Fri, Nov 8, 2013 at 2:55 AM, Kenlee Nakasugi <[hidden email]> wrote:
Hi again,

I updated our gbrowse instance with a new database. When I select it from the 'data source' drop down list, the first page it displays is a search result rather than the Overview/Region/Details panes.
Our other versions load correctly.
You can view it here: http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/

I checked the config files and they seem to be ok. I even commented out the 'examples' and 'initial landmark' options, cleared the database cache, reinstalled the database.

I'm not sure why this is happening - the only thing I can think of is that maybe there are non-unique entries in the fasta or gff file and it's having trouble selecting the right one to display. But i checked and they seem ok.

Any advice on what might be causing this?

Thanks,
Ken

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

Kenlee Nakasugi

Rm873, Bldg-G08 (level 8)
School of Molecular Bioscience
University of New South Wales
Ph: 02-9114-1321

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
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Re: selecting data source results in a search result

Scott Cain
Hi Ken,

I would be reluctant to include the reset parameter in redirects because GBrowse does use cookies for maintaining a user's last state, which is great for users (it can be irritating for devs and admins trying to debug problems though :-)

Scott



On Fri, Nov 8, 2013 at 5:56 PM, Kenlee Nakasugi <[hidden email]> wrote:
Hi Scott,

Hmm that's weird because I had tried it on multiple computers at home and work looking at that database page for the first time (I had looked at v03 database from these computers previously though).
Anyway reset=1 did the trick. I might include this in all redirects.

Thanks
Ken



From: Scott Cain [[hidden email]]
Sent: Saturday, November 09, 2013 2:17 AM
To: Kenlee Nakasugi
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] selecting data source results in a search result

Hi Ken,

I suspect you have a cookie that is causing that behavior, because when I go to your link, I get an initial empty page that I would expect (screenshot attached).  Try going to this url to reset the cookies:


Scott



On Fri, Nov 8, 2013 at 2:55 AM, Kenlee Nakasugi <[hidden email]> wrote:
Hi again,

I updated our gbrowse instance with a new database. When I select it from the 'data source' drop down list, the first page it displays is a search result rather than the Overview/Region/Details panes.
Our other versions load correctly.
You can view it here: http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/

I checked the config files and they seem to be ok. I even commented out the 'examples' and 'initial landmark' options, cleared the database cache, reinstalled the database.

I'm not sure why this is happening - the only thing I can think of is that maybe there are non-unique entries in the fasta or gff file and it's having trouble selecting the right one to display. But i checked and they seem ok.

Any advice on what might be causing this?

Thanks,
Ken

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

Kenlee Nakasugi

Rm873, Bldg-G08 (level 8)
School of Molecular Bioscience
University of New South Wales
Ph: 02-9114-1321

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: selecting data source results in a search result

Kenlee Nakasugi-2
Hi Scott,

Sorry to revive this thread, but a problem still persists.
If you go to

http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05

and click on the Examples coordinate, it will take you to a search page instead of the landing page for those coordinates. In fact, if you click on links in the 'Position' column in the results, it will just keep looping in that search page. The only way to get out of it is to click on one of links in the 'Name' column.

This does not happen with
http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv03


It's happening even after i reset cookies.

I'm not sure what is going on - obviously it has something to do with that database, but I should have processed it the same way as v3.

Any ideas to troubleshoot?

Thanks,
Ken


________________________________________
From: Scott Cain [[hidden email]]
Sent: Saturday, November 09, 2013 11:55 AM
To: Kenlee Nakasugi
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] selecting data source results in a search result

Hi Ken,

I would be reluctant to include the reset parameter in redirects because GBrowse does use cookies for maintaining a user's last state, which is great for users (it can be irritating for devs and admins trying to debug problems though :-)

Scott



On Fri, Nov 8, 2013 at 5:56 PM, Kenlee Nakasugi <[hidden email]<mailto:[hidden email]>> wrote:
Hi Scott,

Hmm that's weird because I had tried it on multiple computers at home and work looking at that database page for the first time (I had looked at v03 database from these computers previously though).
Anyway reset=1 did the trick. I might include this in all redirects.

Thanks
Ken


________________________________
From: Scott Cain [[hidden email]<mailto:[hidden email]>]
Sent: Saturday, November 09, 2013 2:17 AM
To: Kenlee Nakasugi
Cc: [hidden email]<mailto:[hidden email]>
Subject: Re: [Gmod-gbrowse] selecting data source results in a search result

Hi Ken,

I suspect you have a cookie that is causing that behavior, because when I go to your link, I get an initial empty page that I would expect (screenshot attached).  Try going to this url to reset the cookies:

  http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/?reset=1

Scott



On Fri, Nov 8, 2013 at 2:55 AM, Kenlee Nakasugi <[hidden email]<mailto:[hidden email]>> wrote:
Hi again,

I updated our gbrowse instance with a new database. When I select it from the 'data source' drop down list, the first page it displays is a search result rather than the Overview/Region/Details panes.
Our other versions load correctly.
You can view it here: http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/

I checked the config files and they seem to be ok. I even commented out the 'examples' and 'initial landmark' options, cleared the database cache, reinstalled the database.

I'm not sure why this is happening - the only thing I can think of is that maybe there are non-unique entries in the fasta or gff file and it's having trouble selecting the right one to display. But i checked and they seem ok.

Any advice on what might be causing this?

Thanks,
Ken

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

Kenlee Nakasugi

Rm873, Bldg-G08 (level 8)
School of Molecular Bioscience
University of New South Wales
Ph: 02-9114-1321

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]<mailto:[hidden email]>
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<tel: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
------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
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Re: selecting data source results in a search result

Scott Cain
Hi Ken,

Can you send the GFF for this scaffold?

Thanks,
Scott


Sent from my iPhone

On Nov 27, 2013, at 12:15 AM, Kenlee Nakasugi <[hidden email]> wrote:

> Hi Scott,
>
> Sorry to revive this thread, but a problem still persists.
> If you go to
>
> http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05
>
> and click on the Examples coordinate, it will take you to a search page instead of the landing page for those coordinates. In fact, if you click on links in the 'Position' column in the results, it will just keep looping in that search page. The only way to get out of it is to click on one of links in the 'Name' column.
>
> This does not happen with
> http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv03
>
>
> It's happening even after i reset cookies.
>
> I'm not sure what is going on - obviously it has something to do with that database, but I should have processed it the same way as v3.
>
> Any ideas to troubleshoot?
>
> Thanks,
> Ken
>
>
> ________________________________________
> From: Scott Cain [[hidden email]]
> Sent: Saturday, November 09, 2013 11:55 AM
> To: Kenlee Nakasugi
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] selecting data source results in a search result
>
> Hi Ken,
>
> I would be reluctant to include the reset parameter in redirects because GBrowse does use cookies for maintaining a user's last state, which is great for users (it can be irritating for devs and admins trying to debug problems though :-)
>
> Scott
>
>
>
> On Fri, Nov 8, 2013 at 5:56 PM, Kenlee Nakasugi <[hidden email]<mailto:[hidden email]>> wrote:
> Hi Scott,
>
> Hmm that's weird because I had tried it on multiple computers at home and work looking at that database page for the first time (I had looked at v03 database from these computers previously though).
> Anyway reset=1 did the trick. I might include this in all redirects.
>
> Thanks
> Ken
>
>
> ________________________________
> From: Scott Cain [[hidden email]<mailto:[hidden email]>]
> Sent: Saturday, November 09, 2013 2:17 AM
> To: Kenlee Nakasugi
> Cc: [hidden email]<mailto:[hidden email]>
> Subject: Re: [Gmod-gbrowse] selecting data source results in a search result
>
> Hi Ken,
>
> I suspect you have a cookie that is causing that behavior, because when I go to your link, I get an initial empty page that I would expect (screenshot attached).  Try going to this url to reset the cookies:
>
>  http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/?reset=1
>
> Scott
>
>
>
> On Fri, Nov 8, 2013 at 2:55 AM, Kenlee Nakasugi <[hidden email]<mailto:[hidden email]>> wrote:
> Hi again,
>
> I updated our gbrowse instance with a new database. When I select it from the 'data source' drop down list, the first page it displays is a search result rather than the Overview/Region/Details panes.
> Our other versions load correctly.
> You can view it here: http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/
>
> I checked the config files and they seem to be ok. I even commented out the 'examples' and 'initial landmark' options, cleared the database cache, reinstalled the database.
>
> I'm not sure why this is happening - the only thing I can think of is that maybe there are non-unique entries in the fasta or gff file and it's having trouble selecting the right one to display. But i checked and they seem ok.
>
> Any advice on what might be causing this?
>
> Thanks,
> Ken
>
> --------------------
>
> Kenlee Nakasugi
>
> Rm873, Bldg-G08 (level 8)
> School of Molecular Bioscience
> University of New South Wales
> Ph: 02-9114-1321
>
> ------------------------------------------------------------------------------
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models. Explore
> techniques for threading, error checking, porting, and tuning. Get the most
> from the latest Intel processors and coprocessors. See abstracts and register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]<mailto:[hidden email]>
> 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<tel: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

------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
_______________________________________________
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Re: selecting data source results in a search result

Kenlee Nakasugi-2
Hi Scott,

I might have found the problem based on your question.
The scaffolds lengths does not correspond to the gff start and end positions. I now need to look at my pipelines.

Glad I asked you.

thanks!
Ken


________________________________________
From: Scott Cain [[hidden email]]
Sent: Wednesday, November 27, 2013 4:35 PM
To: Kenlee Nakasugi
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] selecting data source results in a search result

Hi Ken,

Can you send the GFF for this scaffold?

Thanks,
Scott


Sent from my iPhone

On Nov 27, 2013, at 12:15 AM, Kenlee Nakasugi <[hidden email]> wrote:

> Hi Scott,
>
> Sorry to revive this thread, but a problem still persists.
> If you go to
>
> http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05
>
> and click on the Examples coordinate, it will take you to a search page instead of the landing page for those coordinates. In fact, if you click on links in the 'Position' column in the results, it will just keep looping in that search page. The only way to get out of it is to click on one of links in the 'Name' column.
>
> This does not happen with
> http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv03
>
>
> It's happening even after i reset cookies.
>
> I'm not sure what is going on - obviously it has something to do with that database, but I should have processed it the same way as v3.
>
> Any ideas to troubleshoot?
>
> Thanks,
> Ken
>
>
> ________________________________________
> From: Scott Cain [[hidden email]]
> Sent: Saturday, November 09, 2013 11:55 AM
> To: Kenlee Nakasugi
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] selecting data source results in a search result
>
> Hi Ken,
>
> I would be reluctant to include the reset parameter in redirects because GBrowse does use cookies for maintaining a user's last state, which is great for users (it can be irritating for devs and admins trying to debug problems though :-)
>
> Scott
>
>
>
> On Fri, Nov 8, 2013 at 5:56 PM, Kenlee Nakasugi <[hidden email]<mailto:[hidden email]>> wrote:
> Hi Scott,
>
> Hmm that's weird because I had tried it on multiple computers at home and work looking at that database page for the first time (I had looked at v03 database from these computers previously though).
> Anyway reset=1 did the trick. I might include this in all redirects.
>
> Thanks
> Ken
>
>
> ________________________________
> From: Scott Cain [[hidden email]<mailto:[hidden email]>]
> Sent: Saturday, November 09, 2013 2:17 AM
> To: Kenlee Nakasugi
> Cc: [hidden email]<mailto:[hidden email]>
> Subject: Re: [Gmod-gbrowse] selecting data source results in a search result
>
> Hi Ken,
>
> I suspect you have a cookie that is causing that behavior, because when I go to your link, I get an initial empty page that I would expect (screenshot attached).  Try going to this url to reset the cookies:
>
>  http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/?reset=1
>
> Scott
>
>
>
> On Fri, Nov 8, 2013 at 2:55 AM, Kenlee Nakasugi <[hidden email]<mailto:[hidden email]>> wrote:
> Hi again,
>
> I updated our gbrowse instance with a new database. When I select it from the 'data source' drop down list, the first page it displays is a search result rather than the Overview/Region/Details panes.
> Our other versions load correctly.
> You can view it here: http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/
>
> I checked the config files and they seem to be ok. I even commented out the 'examples' and 'initial landmark' options, cleared the database cache, reinstalled the database.
>
> I'm not sure why this is happening - the only thing I can think of is that maybe there are non-unique entries in the fasta or gff file and it's having trouble selecting the right one to display. But i checked and they seem ok.
>
> Any advice on what might be causing this?
>
> Thanks,
> Ken
>
> --------------------
>
> Kenlee Nakasugi
>
> Rm873, Bldg-G08 (level 8)
> School of Molecular Bioscience
> University of New South Wales
> Ph: 02-9114-1321
>
> ------------------------------------------------------------------------------
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models. Explore
> techniques for threading, error checking, porting, and tuning. Get the most
> from the latest Intel processors and coprocessors. See abstracts and register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]<mailto:[hidden email]>
> 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<tel: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
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Re: selecting data source results in a search result

Kenlee Nakasugi-2
Hi Scott,

Actually, scratch that...  my .fai files (from samtools faidx) numbers were not corresponding to the size annotated in the header for each scaffold, which led to my initial conclusion.
When I actually check the sequence, the .fai files are correct - i.e. the gff3 start/stop positions for the scaffold sizes are correct. Sorry about that.

So back to your original question:

Here's some lines from the v05 scaffold:

##gff-version 3
Nbv0.5scaffold1 Nbenthamianav0.5 scaffold 1 2628400 . . . Name=Nbv0.5scaffold1
Nbv0.5scaffold2 Nbenthamianav0.5 scaffold 1 2313106 . . . Name=Nbv0.5scaffold2
Nbv0.5scaffold3 Nbenthamianav0.5 scaffold 1 2307292 . . . Name=Nbv0.5scaffold3
Nbv0.5scaffold4 Nbenthamianav0.5 scaffold 1 2256521 . . . Name=Nbv0.5scaffold4
Nbv0.5scaffold5 Nbenthamianav0.5 scaffold 1 2201201 . . . Name=Nbv0.5scaffold5


and some from the v03 scaffolds:

##gff-version 3
Nbv0.3scaffold1 NbenthamianaV0.3 scaffold 1 447128 . . . Name=Nbv0.3scaffold1
Nbv0.3scaffold2 NbenthamianaV0.3 scaffold 1 269198 . . . Name=Nbv0.3scaffold2
Nbv0.3scaffold3 NbenthamianaV0.3 scaffold 1 265062 . . . Name=Nbv0.3scaffold3
Nbv0.3scaffold4 NbenthamianaV0.3 scaffold 1 263685 . . . Name=Nbv0.3scaffold4
Nbv0.3scaffold5 NbenthamianaV0.3 scaffold 1 262653 . . . Name=Nbv0.3scaffold5



Thanks,
Ken


_______________________
From: Kenlee Nakasugi [[hidden email]]
Sent: Wednesday, November 27, 2013 5:00 PM
To: Scott Cain
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] selecting data source results in a search result

Hi Scott,

I might have found the problem based on your question.
The scaffolds lengths does not correspond to the gff start and end positions. I now need to look at my pipelines.

Glad I asked you.

thanks!
Ken


________________________________________
From: Scott Cain [[hidden email]]
Sent: Wednesday, November 27, 2013 4:35 PM
To: Kenlee Nakasugi
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] selecting data source results in a search result

Hi Ken,

Can you send the GFF for this scaffold?

Thanks,
Scott


Sent from my iPhone

On Nov 27, 2013, at 12:15 AM, Kenlee Nakasugi <[hidden email]> wrote:

> Hi Scott,
>
> Sorry to revive this thread, but a problem still persists.
> If you go to
>
> http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05
>
> and click on the Examples coordinate, it will take you to a search page instead of the landing page for those coordinates. In fact, if you click on links in the 'Position' column in the results, it will just keep looping in that search page. The only way to get out of it is to click on one of links in the 'Name' column.
>
> This does not happen with
> http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv03
>
>
> It's happening even after i reset cookies.
>
> I'm not sure what is going on - obviously it has something to do with that database, but I should have processed it the same way as v3.
>
> Any ideas to troubleshoot?
>
> Thanks,
> Ken
>
>
> ________________________________________
> From: Scott Cain [[hidden email]]
> Sent: Saturday, November 09, 2013 11:55 AM
> To: Kenlee Nakasugi
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] selecting data source results in a search result
>
> Hi Ken,
>
> I would be reluctant to include the reset parameter in redirects because GBrowse does use cookies for maintaining a user's last state, which is great for users (it can be irritating for devs and admins trying to debug problems though :-)
>
> Scott
>
>
>
> On Fri, Nov 8, 2013 at 5:56 PM, Kenlee Nakasugi <[hidden email]<mailto:[hidden email]>> wrote:
> Hi Scott,
>
> Hmm that's weird because I had tried it on multiple computers at home and work looking at that database page for the first time (I had looked at v03 database from these computers previously though).
> Anyway reset=1 did the trick. I might include this in all redirects.
>
> Thanks
> Ken
>
>
> ________________________________
> From: Scott Cain [[hidden email]<mailto:[hidden email]>]
> Sent: Saturday, November 09, 2013 2:17 AM
> To: Kenlee Nakasugi
> Cc: [hidden email]<mailto:[hidden email]>
> Subject: Re: [Gmod-gbrowse] selecting data source results in a search result
>
> Hi Ken,
>
> I suspect you have a cookie that is causing that behavior, because when I go to your link, I get an initial empty page that I would expect (screenshot attached).  Try going to this url to reset the cookies:
>
>  http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/?reset=1
>
> Scott
>
>
>
> On Fri, Nov 8, 2013 at 2:55 AM, Kenlee Nakasugi <[hidden email]<mailto:[hidden email]>> wrote:
> Hi again,
>
> I updated our gbrowse instance with a new database. When I select it from the 'data source' drop down list, the first page it displays is a search result rather than the Overview/Region/Details panes.
> Our other versions load correctly.
> You can view it here: http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/
>
> I checked the config files and they seem to be ok. I even commented out the 'examples' and 'initial landmark' options, cleared the database cache, reinstalled the database.
>
> I'm not sure why this is happening - the only thing I can think of is that maybe there are non-unique entries in the fasta or gff file and it's having trouble selecting the right one to display. But i checked and they seem ok.
>
> Any advice on what might be causing this?
>
> Thanks,
> Ken
>
> --------------------
>
> Kenlee Nakasugi
>
> Rm873, Bldg-G08 (level 8)
> School of Molecular Bioscience
> University of New South Wales
> Ph: 02-9114-1321
>
> ------------------------------------------------------------------------------
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models. Explore
> techniques for threading, error checking, porting, and tuning. Get the most
> from the latest Intel processors and coprocessors. See abstracts and register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]<mailto:[hidden email]>
> 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<tel: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
------------------------------------------------------------------------------
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Re: selecting data source results in a search result

Kenlee Nakasugi-2
In reply to this post by Scott Cain
Hi Scott,

I've pinpointed the problem to a gff3 file. It's a gff junctions file from tophat. I appended 'Apex' to distinguish from other samples.

e.g.
Nbv0.5scaffold1 Apex BED_feature 288798 290524 23 + . ID=Apex_BED_feature1;Name=Apex_JUNC00000001
Nbv0.5scaffold1 Apex BED_block 288798 288877 23 + . Parent=Apex_BED_feature1;Name=Apex_JUNC00000001
Nbv0.5scaffold1 Apex BED_thick_feature 288798 290524 23 + . Parent=Apex_BED_feature1;Name=Apex_JUNC00000001
Nbv0.5scaffold1 Apex BED_block 290461 290524 23 + . Parent=Apex_BED_feature1;Name=Apex_JUNC00000001

Nbv0.5scaffold1 Apex BED_feature 288883 290479 1 + . ID=Apex_BED_feature2;Name=Apex_JUNC00000002
Nbv0.5scaffold1 Apex BED_block 288883 288950 1 + . Parent=Apex_BED_feature2;Name=Apex_JUNC00000002
Nbv0.5scaffold1 Apex BED_thick_feature 288883 290479 1 + . Parent=Apex_BED_feature2;Name=Apex_JUNC00000002
Nbv0.5scaffold1 Apex BED_block 290461 290479 1 + . Parent=Apex_BED_feature2;Name=Apex_JUNC00000002


Maybe it's because of the two 'BED_block' and 'BED_thick_feature' features, that have exactly the same attributes?
I thought it wouldn't matter as long as there is only one unique Parent?

thanks,
Ken

________________________________________
From: Scott Cain [[hidden email]]
Sent: Wednesday, November 27, 2013 4:35 PM
To: Kenlee Nakasugi
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] selecting data source results in a search result

Hi Ken,

Can you send the GFF for this scaffold?

Thanks,
Scott


Sent from my iPhone

On Nov 27, 2013, at 12:15 AM, Kenlee Nakasugi <[hidden email]> wrote:

> Hi Scott,
>
> Sorry to revive this thread, but a problem still persists.
> If you go to
>
> http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05
>
> and click on the Examples coordinate, it will take you to a search page instead of the landing page for those coordinates. In fact, if you click on links in the 'Position' column in the results, it will just keep looping in that search page. The only way to get out of it is to click on one of links in the 'Name' column.
>
> This does not happen with
> http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv03
>
>
> It's happening even after i reset cookies.
>
> I'm not sure what is going on - obviously it has something to do with that database, but I should have processed it the same way as v3.
>
> Any ideas to troubleshoot?
>
> Thanks,
> Ken
>
>
> ________________________________________
> From: Scott Cain [[hidden email]]
> Sent: Saturday, November 09, 2013 11:55 AM
> To: Kenlee Nakasugi
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] selecting data source results in a search result
>
> Hi Ken,
>
> I would be reluctant to include the reset parameter in redirects because GBrowse does use cookies for maintaining a user's last state, which is great for users (it can be irritating for devs and admins trying to debug problems though :-)
>
> Scott
>
>
>
> On Fri, Nov 8, 2013 at 5:56 PM, Kenlee Nakasugi <[hidden email]<mailto:[hidden email]>> wrote:
> Hi Scott,
>
> Hmm that's weird because I had tried it on multiple computers at home and work looking at that database page for the first time (I had looked at v03 database from these computers previously though).
> Anyway reset=1 did the trick. I might include this in all redirects.
>
> Thanks
> Ken
>
>
> ________________________________
> From: Scott Cain [[hidden email]<mailto:[hidden email]>]
> Sent: Saturday, November 09, 2013 2:17 AM
> To: Kenlee Nakasugi
> Cc: [hidden email]<mailto:[hidden email]>
> Subject: Re: [Gmod-gbrowse] selecting data source results in a search result
>
> Hi Ken,
>
> I suspect you have a cookie that is causing that behavior, because when I go to your link, I get an initial empty page that I would expect (screenshot attached).  Try going to this url to reset the cookies:
>
>  http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/?reset=1
>
> Scott
>
>
>
> On Fri, Nov 8, 2013 at 2:55 AM, Kenlee Nakasugi <[hidden email]<mailto:[hidden email]>> wrote:
> Hi again,
>
> I updated our gbrowse instance with a new database. When I select it from the 'data source' drop down list, the first page it displays is a search result rather than the Overview/Region/Details panes.
> Our other versions load correctly.
> You can view it here: http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/
>
> I checked the config files and they seem to be ok. I even commented out the 'examples' and 'initial landmark' options, cleared the database cache, reinstalled the database.
>
> I'm not sure why this is happening - the only thing I can think of is that maybe there are non-unique entries in the fasta or gff file and it's having trouble selecting the right one to display. But i checked and they seem ok.
>
> Any advice on what might be causing this?
>
> Thanks,
> Ken
>
> --------------------
>
> Kenlee Nakasugi
>
> Rm873, Bldg-G08 (level 8)
> School of Molecular Bioscience
> University of New South Wales
> Ph: 02-9114-1321
>
> ------------------------------------------------------------------------------
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models. Explore
> techniques for threading, error checking, porting, and tuning. Get the most
> from the latest Intel processors and coprocessors. See abstracts and register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]<mailto:[hidden email]>
> 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<tel: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

------------------------------------------------------------------------------
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organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
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Re: selecting data source results in a search result

Kenlee Nakasugi-2
Hi Scott,

I've solved the issue. The problem was the presence of the "##sequence-region" pragma in some gff3 files, which I guess was cause some conflicts with perhaps the scaffolds gff.
If you could comment on this for my education, that would be great, but anyway, issue solved.

Thanks
Ken

________________________________________
From: Kenlee Nakasugi [[hidden email]]
Sent: Friday, November 29, 2013 3:13 PM
To: Scott Cain
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] selecting data source results in a search result

Hi Scott,

I've pinpointed the problem to a gff3 file. It's a gff junctions file from tophat. I appended 'Apex' to distinguish from other samples.

e.g.
Nbv0.5scaffold1 Apex    BED_feature     288798  290524  23      +       .       ID=Apex_BED_feature1;Name=Apex_JUNC00000001
Nbv0.5scaffold1 Apex    BED_block       288798  288877  23      +       .       Parent=Apex_BED_feature1;Name=Apex_JUNC00000001
Nbv0.5scaffold1 Apex    BED_thick_feature       288798  290524  23      +       .       Parent=Apex_BED_feature1;Name=Apex_JUNC00000001
Nbv0.5scaffold1 Apex    BED_block       290461  290524  23      +       .       Parent=Apex_BED_feature1;Name=Apex_JUNC00000001

Nbv0.5scaffold1 Apex    BED_feature     288883  290479  1       +       .       ID=Apex_BED_feature2;Name=Apex_JUNC00000002
Nbv0.5scaffold1 Apex    BED_block       288883  288950  1       +       .       Parent=Apex_BED_feature2;Name=Apex_JUNC00000002
Nbv0.5scaffold1 Apex    BED_thick_feature       288883  290479  1       +       .       Parent=Apex_BED_feature2;Name=Apex_JUNC00000002
Nbv0.5scaffold1 Apex    BED_block       290461  290479  1       +       .       Parent=Apex_BED_feature2;Name=Apex_JUNC00000002


Maybe it's because of the two 'BED_block' and 'BED_thick_feature' features, that have exactly the same attributes?
I thought it wouldn't matter as long as there is only one unique Parent?

thanks,
Ken

________________________________________
From: Scott Cain [[hidden email]]
Sent: Wednesday, November 27, 2013 4:35 PM
To: Kenlee Nakasugi
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] selecting data source results in a search result

Hi Ken,

Can you send the GFF for this scaffold?

Thanks,
Scott


Sent from my iPhone

On Nov 27, 2013, at 12:15 AM, Kenlee Nakasugi <[hidden email]> wrote:

> Hi Scott,
>
> Sorry to revive this thread, but a problem still persists.
> If you go to
>
> http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05
>
> and click on the Examples coordinate, it will take you to a search page instead of the landing page for those coordinates. In fact, if you click on links in the 'Position' column in the results, it will just keep looping in that search page. The only way to get out of it is to click on one of links in the 'Name' column.
>
> This does not happen with
> http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv03
>
>
> It's happening even after i reset cookies.
>
> I'm not sure what is going on - obviously it has something to do with that database, but I should have processed it the same way as v3.
>
> Any ideas to troubleshoot?
>
> Thanks,
> Ken
>
>
> ________________________________________
> From: Scott Cain [[hidden email]]
> Sent: Saturday, November 09, 2013 11:55 AM
> To: Kenlee Nakasugi
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] selecting data source results in a search result
>
> Hi Ken,
>
> I would be reluctant to include the reset parameter in redirects because GBrowse does use cookies for maintaining a user's last state, which is great for users (it can be irritating for devs and admins trying to debug problems though :-)
>
> Scott
>
>
>
> On Fri, Nov 8, 2013 at 5:56 PM, Kenlee Nakasugi <[hidden email]<mailto:[hidden email]>> wrote:
> Hi Scott,
>
> Hmm that's weird because I had tried it on multiple computers at home and work looking at that database page for the first time (I had looked at v03 database from these computers previously though).
> Anyway reset=1 did the trick. I might include this in all redirects.
>
> Thanks
> Ken
>
>
> ________________________________
> From: Scott Cain [[hidden email]<mailto:[hidden email]>]
> Sent: Saturday, November 09, 2013 2:17 AM
> To: Kenlee Nakasugi
> Cc: [hidden email]<mailto:[hidden email]>
> Subject: Re: [Gmod-gbrowse] selecting data source results in a search result
>
> Hi Ken,
>
> I suspect you have a cookie that is causing that behavior, because when I go to your link, I get an initial empty page that I would expect (screenshot attached).  Try going to this url to reset the cookies:
>
>  http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/?reset=1
>
> Scott
>
>
>
> On Fri, Nov 8, 2013 at 2:55 AM, Kenlee Nakasugi <[hidden email]<mailto:[hidden email]>> wrote:
> Hi again,
>
> I updated our gbrowse instance with a new database. When I select it from the 'data source' drop down list, the first page it displays is a search result rather than the Overview/Region/Details panes.
> Our other versions load correctly.
> You can view it here: http://benth-web-pro-1.ucc.usyd.edu.au/fgb2/gbrowse/benthv05/
>
> I checked the config files and they seem to be ok. I even commented out the 'examples' and 'initial landmark' options, cleared the database cache, reinstalled the database.
>
> I'm not sure why this is happening - the only thing I can think of is that maybe there are non-unique entries in the fasta or gff file and it's having trouble selecting the right one to display. But i checked and they seem ok.
>
> Any advice on what might be causing this?
>
> Thanks,
> Ken
>
> --------------------
>
> Kenlee Nakasugi
>
> Rm873, Bldg-G08 (level 8)
> School of Molecular Bioscience
> University of New South Wales
> Ph: 02-9114-1321
>
> ------------------------------------------------------------------------------
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models. Explore
> techniques for threading, error checking, porting, and tuning. Get the most
> from the latest Intel processors and coprocessors. See abstracts and register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]<mailto:[hidden email]>
> 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<tel: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

------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
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