[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 1:59:27 PM
> Subject: Re: [BioC] SomaticSignatures
> 
> 
> 
> ----- 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)
#oops, you need to do this here:
library(tools)
library(utils)

Dan

> 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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