[BioC] SomaticSignatures

[Dan Tenenbaum]

----- Original Message -----
> From: "Steve Lianoglou" <lianoglou.steve at gene.com>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: "Huma Asif" <humaasif79 at yahoo.com>, "bioconductor at r-project.org list" <bioconductor at r-project.org>
> Sent: Thursday, March 27, 2014 1:45:18 PM
> Subject: Re: [BioC] SomaticSignatures
> 
> On Thu, Mar 27, 2014 at 1:39 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
> wrote:
> [snip]
> >>
> >> 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.
> 
> I see.
> 
> >
> > Though usually we direct people in the opposite direction, this
> > StackOverflow post may help:
> >
> > https://stackoverflow.com/questions/19268515/installing-bioconductor-without-internet/19269962#19269962
> >
> > 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:
> >
> > http://www.bioconductor.org/about/mirrors/mirror-how-to/
> 
> An altertnative would be to "cheat" and follow along with what
> Vincent did.
> 
> You could start on your own machine w/ a brand new empty R-3.1-alpha
> install.
> 
> Then do:
> 
> R> source('http://bioconductor.org/biocLite.R')
> R> biocLite('SomaticSignatures')
> 
> You will then see all of the packages that were downloaded to satisfy
> the dependency tree required for the installation (here are just
> three
> of them that Vincent required):
> 
> """
> trying URL 'http://cran.fhcrc.org/src/contrib/gridBase_0.4-7.tar.gz'
> Content type 'application/x-gzip' length 153373 bytes (149 Kb)
> opened URL
> ==================================================
> downloaded 149 Kb
> 
> trying URL 'http://cran.fhcrc.org/src/contrib/NMF_0.20.5.tar.gz'
> Content type 'application/x-gzip' length 1763782 bytes (1.7 Mb)
> opened URL
> ==================================================
> downloaded 1.7 Mb
> 
> trying URL '
> http://bioconductor.org/packages/2.14/bioc/src/contrib/pcaMethods_1.53.4.tar.gz
> '
> """
> 
> Now you have the packages required (here he needed gridBase, NMF and
> pcaMethods) *as well as* the URLs required to download them.
> 
> Go back and pull out all of the URLs
> 
> Download the packages.
> 

A trick I learned from Martin yesterday may help with this step (eliminating the need to know URLs):

library(BiocInstaller)
download.packages(c("SomaticSignatures", "gridBase", "NMF", "pcaMethods"),
repos=biocinstallRepos(), type="source")

This will download all the source package tarballs to your current directory.

As Steve and Vince point out, your actual list of packages that you'd need to download would be longer.

I think there is another trick to tell you the recursive dependencies of a package, but I don't know if off the top of my head.

Dan


> Move them over to your cluster.
> 
> Then install by the command line as you like *into R-3.1-alpha*
> 
> HTH,
> -steve
> 
> --
> Steve Lianoglou
> Computational Biologist
> Genentech
>