[BioC] SomaticSignatures

Dan Tenenbaum dtenenba at fhcrc.org
Thu Mar 27 21:39:28 CET 2014

----- Original Message -----
> From: "Steve Lianoglou" <lianoglou.steve at gene.com>
> To: "Huma Asif" <humaasif79 at yahoo.com>
> Cc: "bioconductor at r-project.org list" <bioconductor at r-project.org>
> Sent: Thursday, March 27, 2014 1:34:01 PM
> Subject: Re: [BioC] SomaticSignatures
> Hi,
> On 27 Mar 2014, at 13:01, Huma Asif wrote:
> > Hi
> > Though i installed variant annotation and R vesion as suggested.
> > every
> > package seems dependent on other like somatic signature
> > ....mutationcontext..... variantannotation......GRanges....h5vc
> > package.
> That's why installation functions (like biocLite) are made available.
> They handle the dependency chasing for you.
> > It seems impossible
> It's not impossible, you just need to do a lot of book keeping
> regarding
> the dependency structure of the packages SomaticSignatures depends on
> (and the packages those packages depend on) if you insist on
> installing
> this manually.
> Why is installing it via `biocLite('SomaticSignatures')` out of the
> question here? You obviously have access to an internet connection --
> you are sending email and downloading the dependent packages by hand
> --
> so, why don't you just install it that way?

I think the machine in question (a cluster?) has no direct access to the internet, so packages
must be downloaded to some other machine and then copied there.

Though usually we direct people in the opposite direction, this StackOverflow post may help:


If the machine that has internet and the machine that doesn't are similar enough and have the same libraries installed, this could work. You could also create your own internal CRAN and BioC mirrors though this may be overkill, but our mirror page will provide more info:



> > I need  to know is there any other package that can help in
> > signatures extraction from vcf files with out being dependent on R.
> It looks like they are "just" creating a variant-by-sample matrix and
> performing some matrix decomposition on that (SVD, NMF), so if you
> know
> how to do each one of these things individually that does not involve
> R,
> then you're in business.
> -steve
> --
> Steve Lianoglou
> Computational Biologist
> Genentech
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