Transposable Element annotation creation

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Transposable Element annotation creation

Guizard Sébastien
Hello list,

I just installed WebApollo on our server and nearly everything works fine.
Indeed, i am able to create any kind of annotation from a track feature except for "repeat_region" and "transposable_element".

Did I failed WebApollo configuration ?

Thanks
-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France
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Re: Transposable Element annotation creation

Ed Lee
Hi Guizard,

Do you see any error messages in the Tomcat log when you try to create transposable_element and repeat_region annotations?

Cheers,
Ed


On Thu, Mar 13, 2014 at 6:45 AM, Guizard Sébastien <[hidden email]> wrote:
Hello list,

I just installed WebApollo on our server and nearly everything works fine.
Indeed, i am able to create any kind of annotation from a track feature except for "repeat_region" and "transposable_element".

Did I failed WebApollo configuration ?

Thanks
-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France

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Re: Transposable Element annotation creation

Guizard Sébastien
That is the problem, there no Error messages in catalane.out. I don't no where to search !

PS: you can call me sebastien :p

Envoyé à partir de mon smartphone Sony Xperia™

---- Ed Lee a écrit ----

Hi Guizard,

Do you see any error messages in the Tomcat log when you try to create transposable_element and repeat_region annotations?

Cheers,
Ed


On Thu, Mar 13, 2014 at 6:45 AM, Guizard Sébastien <[hidden email]> wrote:
Hello list,

I just installed WebApollo on our server and nearly everything works fine.
Indeed, i am able to create any kind of annotation from a track feature except for "repeat_region" and "transposable_element".

Did I failed WebApollo configuration ?

Thanks
-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France

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Re: Transposable Element annotation creation

Ed Lee
Hi Sebastien =)

Sorry about the name mishap.  Just saw your name in the e-mail header and it showed as "Guizard Sebastien", so I guessed the wrong first name =P

Hmmm, do you see any errors in your browse console?  If you're not seeing any issues on catalina.out, it might be a rendering issue on the client.

Cheers,
Ed


On Thu, Mar 13, 2014 at 12:02 PM, Sébastien Guizard <[hidden email]> wrote:
That is the problem, there no Error messages in catalane.out. I don't no where to search !

PS: you can call me sebastien :p

Envoyé à partir de mon smartphone Sony Xperia™

---- Ed Lee a écrit ----


Hi Guizard,

Do you see any error messages in the Tomcat log when you try to create transposable_element and repeat_region annotations?

Cheers,
Ed


On Thu, Mar 13, 2014 at 6:45 AM, Guizard Sébastien <[hidden email]> wrote:
Hello list,

I just installed WebApollo on our server and nearly everything works fine.
Indeed, i am able to create any kind of annotation from a track feature except for "repeat_region" and "transposable_element".

Did I failed WebApollo configuration ?

Thanks
-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France


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Re: Transposable Element annotation creation

Guizard Sébastien
No problem ;)

The port 8080 is closed, so I can't reach the webapollo server from my place. I send a mail to my workmate and ask him to open this port. If he is not at lab tomorow, It will have to wait until monday ...
I give you an answer when I have it !

Thank already !
Seb


Le 13/03/2014 20:20, Ed Lee a écrit :
Hi Sebastien =)

Sorry about the name mishap.  Just saw your name in the e-mail header and it showed as "Guizard Sebastien", so I guessed the wrong first name =P

Hmmm, do you see any errors in your browse console?  If you're not seeing any issues on catalina.out, it might be a rendering issue on the client.

Cheers,
Ed


On Thu, Mar 13, 2014 at 12:02 PM, Sébastien Guizard <[hidden email]> wrote:
That is the problem, there no Error messages in catalane.out. I don't no where to search !

PS: you can call me sebastien :p

Envoyé à partir de mon smartphone Sony Xperia™

---- Ed Lee a écrit ----


Hi Guizard,

Do you see any error messages in the Tomcat log when you try to create transposable_element and repeat_region annotations?

Cheers,
Ed


On Thu, Mar 13, 2014 at 6:45 AM, Guizard Sébastien <[hidden email]> wrote:
Hello list,

I just installed WebApollo on our server and nearly everything works fine.
Indeed, i am able to create any kind of annotation from a track feature except for "repeat_region" and "transposable_element".

Did I failed WebApollo configuration ?

Thanks
-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France




-- 
Sébastien Guizard - PHD Student
"Je sert la science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France
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Re: Transposable Element annotation creation

Guizard Sébastien
Hi,

I discover that i can create transposable element annotation only from match part features.
Here an example :
http://derp.co.uk/ef3ce

When I try with a match feature i get an error in the AnnotTrack.js script (line 1119) :
http://derp.co.uk/82320

Seb

Le 13/03/2014 21:44, Sébastien Guizard a écrit :
No problem ;)

The port 8080 is closed, so I can't reach the webapollo server from my place. I send a mail to my workmate and ask him to open this port. If he is not at lab tomorow, It will have to wait until monday ...
I give you an answer when I have it !

Thank already !
Seb


Le 13/03/2014 20:20, Ed Lee a écrit :
Hi Sebastien =)

Sorry about the name mishap.  Just saw your name in the e-mail header and it showed as "Guizard Sebastien", so I guessed the wrong first name =P

Hmmm, do you see any errors in your browse console?  If you're not seeing any issues on catalina.out, it might be a rendering issue on the client.

Cheers,
Ed


On Thu, Mar 13, 2014 at 12:02 PM, Sébastien Guizard <[hidden email]> wrote:
That is the problem, there no Error messages in catalane.out. I don't no where to search !

PS: you can call me sebastien :p

Envoyé à partir de mon smartphone Sony Xperia™

---- Ed Lee a écrit ----


Hi Guizard,

Do you see any error messages in the Tomcat log when you try to create transposable_element and repeat_region annotations?

Cheers,
Ed


On Thu, Mar 13, 2014 at 6:45 AM, Guizard Sébastien <[hidden email]> wrote:
Hello list,

I just installed WebApollo on our server and nearly everything works fine.
Indeed, i am able to create any kind of annotation from a track feature except for "repeat_region" and "transposable_element".

Did I failed WebApollo configuration ?

Thanks
-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France




-- 
Sébastien Guizard - PHD Student
"Je sert la science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France

-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France
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Re: Transposable Element annotation creation

Colin
Hi Sebastian,
Thanks for finding and reporting this issue. I am able to reproduce this problem and I found a preliminary fix that I am testing now. It seems that we can now create transposable_element annotations with both match and match_part pieces. I'll check with Ed Lee and see if we can get this fix pushed out to our next release.
If you would like a patch I will see if we can arrange for that too.



-Colin
Research Analyst, Dept. of Animal Science
University of Missouri


On Mon, Mar 17, 2014 at 3:44 AM, Guizard Sébastien <[hidden email]> wrote:
Hi,

I discover that i can create transposable element annotation only from match part features.
Here an example :
http://derp.co.uk/ef3ce

When I try with a match feature i get an error in the AnnotTrack.js script (line 1119) :
http://derp.co.uk/82320

Seb

Le 13/03/2014 21:44, Sébastien Guizard a écrit :
No problem ;)

The port 8080 is closed, so I can't reach the webapollo server from my place. I send a mail to my workmate and ask him to open this port. If he is not at lab tomorow, It will have to wait until monday ...
I give you an answer when I have it !

Thank already !
Seb


Le 13/03/2014 20:20, Ed Lee a écrit :
Hi Sebastien =)

Sorry about the name mishap.  Just saw your name in the e-mail header and it showed as "Guizard Sebastien", so I guessed the wrong first name =P

Hmmm, do you see any errors in your browse console?  If you're not seeing any issues on catalina.out, it might be a rendering issue on the client.

Cheers,
Ed


On Thu, Mar 13, 2014 at 12:02 PM, Sébastien Guizard <[hidden email]> wrote:
That is the problem, there no Error messages in catalane.out. I don't no where to search !

PS: you can call me sebastien :p

Envoyé à partir de mon smartphone Sony Xperia™

---- Ed Lee a écrit ----


Hi Guizard,

Do you see any error messages in the Tomcat log when you try to create transposable_element and repeat_region annotations?

Cheers,
Ed


On Thu, Mar 13, 2014 at 6:45 AM, Guizard Sébastien <[hidden email]> wrote:
Hello list,

I just installed WebApollo on our server and nearly everything works fine.
Indeed, i am able to create any kind of annotation from a track feature except for "repeat_region" and "transposable_element".

Did I failed WebApollo configuration ?

Thanks
-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France




-- 
Sébastien Guizard - PHD Student
"Je sert la science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France

-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France

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Re: Transposable Element annotation creation

Guizard Sébastien
Hi,

You're welcome !
A patch would be appreciate, if it's possible of course !

Thanks

Seb


Le 17/03/2014 16:09, Colin a écrit :
Hi Sebastian,
Thanks for finding and reporting this issue. I am able to reproduce this problem and I found a preliminary fix that I am testing now. It seems that we can now create transposable_element annotations with both match and match_part pieces. I'll check with Ed Lee and see if we can get this fix pushed out to our next release.
If you would like a patch I will see if we can arrange for that too.



-Colin
Research Analyst, Dept. of Animal Science
University of Missouri


On Mon, Mar 17, 2014 at 3:44 AM, Guizard Sébastien <[hidden email]> wrote:
Hi,

I discover that i can create transposable element annotation only from match part features.
Here an example :
http://derp.co.uk/ef3ce

When I try with a match feature i get an error in the AnnotTrack.js script (line 1119) :
http://derp.co.uk/82320

Seb

Le 13/03/2014 21:44, Sébastien Guizard a écrit :
No problem ;)

The port 8080 is closed, so I can't reach the webapollo server from my place. I send a mail to my workmate and ask him to open this port. If he is not at lab tomorow, It will have to wait until monday ...
I give you an answer when I have it !

Thank already !
Seb


Le 13/03/2014 20:20, Ed Lee a écrit :
Hi Sebastien =)

Sorry about the name mishap.  Just saw your name in the e-mail header and it showed as "Guizard Sebastien", so I guessed the wrong first name =P

Hmmm, do you see any errors in your browse console?  If you're not seeing any issues on catalina.out, it might be a rendering issue on the client.

Cheers,
Ed


On Thu, Mar 13, 2014 at 12:02 PM, Sébastien Guizard <[hidden email]> wrote:
That is the problem, there no Error messages in catalane.out. I don't no where to search !

PS: you can call me sebastien :p

Envoyé à partir de mon smartphone Sony Xperia™

---- Ed Lee a écrit ----


Hi Guizard,

Do you see any error messages in the Tomcat log when you try to create transposable_element and repeat_region annotations?

Cheers,
Ed


On Thu, Mar 13, 2014 at 6:45 AM, Guizard Sébastien <[hidden email]> wrote:
Hello list,

I just installed WebApollo on our server and nearly everything works fine.
Indeed, i am able to create any kind of annotation from a track feature except for "repeat_region" and "transposable_element".

Did I failed WebApollo configuration ?

Thanks
-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France




-- 
Sébastien Guizard - PHD Student
"Je sert la science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France

-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France


-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France
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Re: Transposable Element annotation creation

Ed Lee
Hi Sebastien,

Colin's patch will be included in the next release, which will be coming out soon.

Cheers,
Ed


On Tue, Mar 18, 2014 at 2:01 AM, Guizard Sébastien <[hidden email]> wrote:
Hi,

You're welcome !
A patch would be appreciate, if it's possible of course !

Thanks

Seb


Le 17/03/2014 16:09, Colin a écrit :
Hi Sebastian,
Thanks for finding and reporting this issue. I am able to reproduce this problem and I found a preliminary fix that I am testing now. It seems that we can now create transposable_element annotations with both match and match_part pieces. I'll check with Ed Lee and see if we can get this fix pushed out to our next release.
If you would like a patch I will see if we can arrange for that too.



-Colin
Research Analyst, Dept. of Animal Science
University of Missouri


On Mon, Mar 17, 2014 at 3:44 AM, Guizard Sébastien <[hidden email]> wrote:
Hi,

I discover that i can create transposable element annotation only from match part features.
Here an example :
http://derp.co.uk/ef3ce

When I try with a match feature i get an error in the AnnotTrack.js script (line 1119) :
http://derp.co.uk/82320

Seb

Le 13/03/2014 21:44, Sébastien Guizard a écrit :
No problem ;)

The port 8080 is closed, so I can't reach the webapollo server from my place. I send a mail to my workmate and ask him to open this port. If he is not at lab tomorow, It will have to wait until monday ...
I give you an answer when I have it !

Thank already !
Seb


Le 13/03/2014 20:20, Ed Lee a écrit :
Hi Sebastien =)

Sorry about the name mishap.  Just saw your name in the e-mail header and it showed as "Guizard Sebastien", so I guessed the wrong first name =P

Hmmm, do you see any errors in your browse console?  If you're not seeing any issues on catalina.out, it might be a rendering issue on the client.

Cheers,
Ed


On Thu, Mar 13, 2014 at 12:02 PM, Sébastien Guizard <[hidden email]> wrote:
That is the problem, there no Error messages in catalane.out. I don't no where to search !

PS: you can call me sebastien :p

Envoyé à partir de mon smartphone Sony Xperia™

---- Ed Lee a écrit ----


Hi Guizard,

Do you see any error messages in the Tomcat log when you try to create transposable_element and repeat_region annotations?

Cheers,
Ed


On Thu, Mar 13, 2014 at 6:45 AM, Guizard Sébastien <[hidden email]> wrote:
Hello list,

I just installed WebApollo on our server and nearly everything works fine.
Indeed, i am able to create any kind of annotation from a track feature except for "repeat_region" and "transposable_element".

Did I failed WebApollo configuration ?

Thanks
-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France




-- 
Sébastien Guizard - PHD Student
"Je sert la science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France

-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France


-- 
Sébastien Guizard - PHD Student
"Je sers la Science et c'est ma joie" - Disciplus Simplex
UMR INRA-CNRS 7247, Physiologie de la Reproduction et des Comportements (PRC)
Equipe 10, Plasticité Génomique et Expression Phénotypique
Centre INRA de Nouzilly
37380 Nouzilly Cedex - France