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Question: Bioconductor Software download
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gravatar for s.munster
13 months ago by
s.munster20
USA/Oklahoma City
s.munster20 wrote:

I want to install bioconductor onto a computer that does not have (and cannot be connected to) internet access.  Can I use the BiocInstaller package to do this?  Is there somewhere else I can go to get a download of the software?  Thanks in advance!

ADD COMMENTlink written 13 months ago by s.munster20
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gravatar for Martin Morgan
13 months ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

It would help to have additional information about your use case. On a cluster, a typical thing to do is to install the packages on the 'head' node, but use it on the workers, perhaps using .libPaths() and R_LIBS_USER tricks. But maybe you're a system administrator want to have access to the entire Bioc repository 'off-line' to make it easy for your local users to install software that would otherwise be blocked by some arcane institutional policy. Then you would rather create a mirror of our repository and point your users to that, see http://bioconductor.org/about/mirrors/mirror-how-to/

ADD COMMENTlink written 13 months ago by Martin Morgan ♦♦ 21k

  Thank you for your quick response.  The policy where I work for this computer is absolutely no internet access so what I need is a stand-alone installation of the bioconductor software.  

  Is the bioconductor software something separate, or is it a wrap around to install packages like biobase? 

  As far as the installation, we are looking at installing it on the head node and possibly another node after that. Two other questions come up.  The first has to do with how R and bioconductor are autoconfigured when it is unpacked and installed.  Is the autoconfiguration generic, such that we could possibly build a windows compatible portable copy of R with all of the bioconductor packages installed?  Is there a choice to get a copy of the bioconductor software that is MPI compatible as well, so that we can better use it on a cluster?

 

Again, thanks for your help, Susan

ADD REPLYlink written 13 months ago by s.munster20

I have resolved my concerns with the bioconductor software - thanks!

ADD REPLYlink written 13 months ago by s.munster20
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