SNPFileCreator_SNP6

[GenePattern Help Forum]

Greetings,

I am interested in using SNPFileCreator_SNP6 to process CEL file that I have recently got.

GenePattern webpage indicated that SNPFileCreator_SNP6 is available only on public server.

So I looked into public server but there was no SNPFileCreator_SNP6.

Do I need some authentication to have access to it or is it simply unavailable at the moment?

I am sorry if this is an inappropriate question to ask here

Thank you

[Barbara Hill]

Hello

The SNPFileCreator_SNP6 is part of the CopyNumberInferencePipeline, and is intended to be run as part of that pipeline, rather than as a standalone module.

Unfortunately, that pipeline is currently non-functional due to a fire in our data center in June, 2018.

Additionally, SNPFileCreator_SNP6 requires a specific environment to run, as indicated in its documentation:

SNPFileCreator_SNP6 requires on average a minimum of 12GB RAM to process SNP

Array 6.0 files. Use the GenePattern public server or configure your local GenePattern

server to allocate the required memory for the module. Note that this module is currently

only supported on 64-bit Linux servers and is therefore not available for download in the

GenePattern Module Repository. 

That being said, I have linked to it here, in-case it is still of use to you.

ftp://gpftp.broadinstitute.org/modules/SNPFileCreator_SNP6.zip

Best

-Barbara