search for: samtool

...nstead of multi-arch? (the sentence below as strictly speaking wrong - the R package was cross-compiled to multi-arch rather than universal). FYI a few other not-so-relevant things but may be useful to some. -------- Original Message -------- Subject: Mac OS X builds of CelQuantileNorm, vcftools/samtools/tabix, and snpStats Date: Wed, 14 Mar 2012 02:59:42 +0000 (GMT) From: Hin-Tak Leung <htl10 at users.sourceforge.net> Reply-To: htl10 at users.sourceforge.net To: bonsai list <outmodedbonsai-announce at lists.sourceforge.net> CelQantileNorm, vcftools/samtools/tabix are bult for Mac OS...

...56165.20 255562.3 68524.45 237479.3 68813.99 209901.8 73147.73 217020.4 70855.45 The bad news is that I've been able to replicate the failures that JF has seen. The workflow starts normally but then eats up free RAM as KT's workflow saturates the nodes with about 26 instances of samtools which does a LOT of IO (10s of GB in the ~30m of the run). This was the case even when I increased the number of nfsd's to 16 and even 32. When using native gluster, the workflow goes to completion in about 23 hrs - about the same as when KT executed it on his machine (using NFS I think.....

Dear folks, Please welcome a newbie both to R and the mailing list :). I am currently working on a sequencing project, and heard about R as well as some of its packages for next gen sequencing, and decided to give it a try. Starting with ShortRead, I found a document (http://www.bioconductor.org/packages/2.5/bioc/vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf) which does mention