[Bioc-devel] Installing Annotation Packages Matching a Pattern

[Martin Morgan]

The BiocInstaller package

  library(BiocInstaller)

defines appropriate repositories biocinstallRepos() that can be queried for available packages that are named consistently with your needs

  nms = row.names(available.packages(contrib.url(biocinstallRepos())))
  want = grep("Hsapiens|Mmusculus", nms, value=TRUE)

(there are about 30 of these; maybe you don't want them all?) and retrieved using biocLite

  biocLite(want)

It might also be interesting to identify relevant AnnotationHub resources, e.g., in devel

  library(AnnotationHub)
  hub = AnnotationHub()

and query (in devel; in release you would use metadata(hub) and search through that) to discover the 5339 relevant resources

> query(hub, "sapiens")
class: AnnotationHub 
length: 5339 
filters: none 
hubUrl: http://annotationhub.bioconductor.org/ah 
snapshotVersion: 3.0/1.5.3; snapshotDate: 2014-04-01
hubCache: /home/mtmorgan/.AnnotationHub 

Martin
----- Dario Strbenac <dstr7320 at uni.sydney.edu.au> wrote:
> Hello,
> 
> I would like to install all software packages and also all annotation packages containing the pattern Hsapiens or Mmusculus in their name. I know about biocLite(all_group()) to do the first task, but I'm not sure if it's possible to query the repository with a pattern. The installation guide simply advises "Visit the Workflows page and software package list to discover available packages."
> 
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
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