[BioC] SomaticSignatures

[Dan Tenenbaum]

----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> To: "Steve Lianoglou" <lianoglou.steve at gene.com>
> Cc: "Huma Asif" <humaasif79 at yahoo.com>, "bioconductor at r-project.org list" <bioconductor at r-project.org>
> Sent: Thursday, March 27, 2014 1:49:13 PM
> Subject: Re: [BioC] SomaticSignatures
> 
> 
> 
> ----- 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.

Here it is:

library(BiocInstaller)
pdb <- available.packages(contrib.url(biocinstallRepos()))
pkgs <- unlist(unname(package_dependencies("SomaticSignatures", db=pdb)))

Then use pkgs as the first argument to download.packages() above.
Dan


> 
> 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
> >
> 
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