I was wondering if anyone had tried running GATK and associated software on a PCI-e flash card for example FusionIO?
This would be in relation to heart research although I am not sure that is relevant.
Thanks for the offer @james007, but at the moment we're all tied up in projects. We'd love to hear how it goes when you try it though.
We prefer to keep all communications on this forum unless there are confidentiality concerns. If there are, we can use private messages and emails if necessary.
We have not tried it at the Broad, and unfortunately we cannot guarantee that it will work.
I am going to have a test cluster setup next week (hopefully) perhaps you would be interested in a remote log on. ?
ok, is it best to communicate via this portal or do you have an email address also?
Cards arriving monday... SHould have FusionIO cards as well to compare..
Collaborators should also be posting comments soon. www.dnadata.co
We are installing the Memblaze cards today and this lot....
We might test FusionIO, and Altera FPGA afterwards as we have stack installed.
Centos latest version
GATK v3.2 : https://www.broadinstitute.org/gatk/
perl v5.8.8 or higher : https://www.perl.org/get.html
bwa v0.7.10-r789 : http://sourceforge.net/projects/bio-bwa/files/
picard-tools-1.117 : http://broadinstitute.github.io/picard/
fastqc_v0.10.1 : http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
samtools-0.2.0 : http://sourceforge.net/projects/samtools/files/
jdk1.7.0_40 : http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html
snpEff_v3.4e : http://snpeff.sourceforge.net/
BEDTools-Version-2.11.2 : http://bedtools.readthedocs.org/en/latest/content/installation.html
Does GATK have any test data which we can run on the above system. Seems most of this type of data is sensitive and can't be used for a test.
This article may help: http://gatkforums.broadinstitute.org/discussion/1213/whats-in-the-resource-bundle-and-how-can-i-get-it