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 Administrative Assistant: [email protected] This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. From: Jorge Zamora <[email protected]<mailto:[email protected]>> Date: Thu, 3 Feb 2011 11:43:44 -0500 To: Elena Rivkin <[email protected]<mailto:[email protected]>>, Arek Kasprzyk <[email protected]<mailto:[email protected]>>, Syed Haider <[email protected]<mailto:[email protected]>>, Junjun Zhang <[email protected]<mailto:[email protected]>> 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----- From: [email protected]<mailto:[email protected]> [mailto:[email protected]] On Behalf Of Jorge Zamora Sent: Thursday, February 03, 2011 4:27 AM To: [email protected]<mailto:[email protected]> 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 **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 [email protected]<mailto:[email protected]> 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. **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.
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