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Question: Bioconductor Software download
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gravatar for susan.munster
7 months ago by
USA/Oklahoma City
susan.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 7 months ago by susan.munster20
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gravatar for Martin Morgan
7 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k 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 7 months ago by Martin Morgan ♦♦ 20k

  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 7 months ago by susan.munster20

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

ADD REPLYlink written 6 months ago by susan.munster20
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