[BioMart Users] unable to retrieve simple mutations with rc4

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[BioMart Users] unable to retrieve simple mutations with rc4

Jorge Zamora-2

        Hello,



        I just set up the ICGC mart using rc4. I'm unable to retrieve
        simple mutations while samples, genes, CNVs seem to work fine.


        is there anybody else experiencing a similar situation?



        Thanks,


        Jorge




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Re: [BioMart Users] unable to retrieve simple mutations with rc4

Arek Kasprzyk-2

Hi Jorge,
Please use icgc3.xml. This is the right config. 
Syed: we need to remove icgc3_central from the branch, It is confusing


a




Arek Kasprzyk
Director, Bioinformatics Operations and Principal Investigator

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3
     
Tel:       416-673-8559
Toll-free:           1-866-678-6427
www.oicr.on.ca


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From: Jorge Zamora <[hidden email]>
Date: Thu, 3 Feb 2011 11:43:44 -0500
To: Elena Rivkin <[hidden email]>, Arek Kasprzyk <[hidden email]>, Syed Haider <[hidden email]>, Junjun Zhang <[hidden email]>
Subject: Re: [BioMart Users] unable to retrieve simple mutations with rc4




I made a bit of research I found out that I'm able to retrieve 'simple
mutations' with rc4 using the 'Flexible' or 'Advanced' interfaces if I
do *NOT* select all the attributes!! I can see that the 'Quick'
interface has enabled all the attributes by default and that may the
reason why I don't get results.


One question, in rc4 there was an icgc3_central.xml, however I'm using
the icgc3.xml for the configuration, is that OK?

Thanks,
Jorge


Jorge Zamora wrote:
Hello Elena,

Basically today I've

- re-insatelled rc3 and rc4
- even moved my ICGC mart database to my local machine
- configured the xml file and run it using rc3 and works fine
- use the same xml in rc4 and the simple mutations don't show up!

For some reason the problem using rc4 affect the retrieval of simple
mutations, no only the from the URLs but also from my local mart.

In rc3 I get the mutations nearly instantaneously. However If I use
rc4 I get the sample data the CNVs but when I select 'simple
mutations' three 'three squares' in the browers stay there forever.

any idea? Can I stick to rc3 in the meantime?

Thanks,
Jorge

Elena Rivkin wrote:
Hi Jorge, Can you specify which cancer types/projects you are
searching. I am not able to reproduce the problem.
Thank you, Elena

-----Original Message-----
Behalf Of Jorge Zamora
Sent: Thursday, February 03, 2011 4:27 AM
Subject: [BioMart Users] unable to retrieve simple mutations with rc4

Hello,

I just set up the ICGC mart using rc4. I'm unable to retrieve simple
mutations while samples, genes, CNVs seem to work fine.

is there anybody else experiencing a similar situation?

Thanks,
Jorge


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correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
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attachments may contain confidential and privileged information for
the sole use of the designated recipient named above. Distribution,
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[BioMart Users] logo/image in biomart 0.8 rc4

Jorge Zamora-2
In reply to this post by Jorge Zamora-2
Hello,

I'm trying to show a logo/image in martview 0.8 rc4 by modifying the
file 'header.html'  located in 'release-0_8-candidate_4/web/includes/'

My question is: what  is the folder where I should place the image
files? I tried in the same folder where the 'header.html' is located but
it does not work


This is my header.html so far:


<style type="text/css">
#biomart-header {
  text-align: center;
}
</style>

<h1>My Page Title</h1>
<a href="http://www.inab.org/" target="_blank"><img src="logo_cnio.png"
border="0" alt= "CNIO" title="CNIO"/></a>


Thanks,
Jorge

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
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Re: [BioMart Users] logo/image in biomart 0.8 rc4

Syed Haider
Hi Jorge,

<img src="/includes/logo_cnio.png">

this should work,

Syed

On 08/02/2011 14:16, Jorge Zamora wrote:

> Hello,
>
> I'm trying to show a logo/image in martview 0.8 rc4 by modifying the
> file 'header.html'  located in 'release-0_8-candidate_4/web/includes/'
>
> My question is: what  is the folder where I should place the image
> files? I tried in the same folder where the 'header.html' is located but
> it does not work
>
>
> This is my header.html so far:
>
>
> <style type="text/css">
> #biomart-header {
>    text-align: center;
> }
> </style>
>
> <h1>My Page Title</h1>
> <a href="http://www.inab.org/" target="_blank"><img src="logo_cnio.png"
> border="0" alt= "CNIO" title="CNIO"/></a>
>
>
> Thanks,
> Jorge
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
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Re: [BioMart Users] logo/image in biomart 0.8 rc4

Jorge Zamora-2
Hi syed,

It worked!

Thanks a lot,
Jorge

Syed Haider wrote:

> Hi Jorge,
>
> <img src="/includes/logo_cnio.png">
>
> this should work,
>
> Syed
>
> On 08/02/2011 14:16, Jorge Zamora wrote:
>> Hello,
>>
>> I'm trying to show a logo/image in martview 0.8 rc4 by modifying the
>> file 'header.html'  located in 'release-0_8-candidate_4/web/includes/'
>>
>> My question is: what  is the folder where I should place the image
>> files? I tried in the same folder where the 'header.html' is located but
>> it does not work
>>
>>
>> This is my header.html so far:
>>
>>
>> <style type="text/css">
>> #biomart-header {
>>    text-align: center;
>> }
>> </style>
>>
>> <h1>My Page Title</h1>
>> <a href="http://www.inab.org/" target="_blank"><img src="logo_cnio.png"
>> border="0" alt= "CNIO" title="CNIO"/></a>
>>
>>
>> Thanks,
>> Jorge
>>
>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso
>> los ficheros adjuntos, pueden contener información protegida para el
>> uso exclusivo de su destinatario. Se prohíbe la distribución,
>> reproducción o cualquier otro tipo de transmisión por parte de otra
>> persona que no sea el destinatario. Si usted recibe por error este
>> correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
>> **CONFIDENTIALITY NOTICE** This email communication and any
>> attachments may contain confidential and privileged information for
>> the sole use of the designated recipient named above. Distribution,
>> reproduction or any other use of this transmission by any party other
>> than the intended recipient is prohibited. If you are not the
>> intended recipient please contact the sender and delete all copies.
>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users


**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
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