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Last pushed: a month ago
Short Description
Basic docker image for ad-hoc genomic analyses
Full Description

docker-genomic-analysis

Basic docker image for ad-hoc genomic analyses - combines a lot of the tools that are handy for exploring data on a ubuntu base image.

Notes:

  • Python 2 and 3 are both installed (using conda)

    • For python 3.6, you'll use python3 (if you are using LSF_DOCKER_PRESERVE_ENVIRONMENT=false, just python will work)
    • For python2.7, run source activate python2, then python
  • R 3.4 and some basic packages are installed. For convenience, it can be useful to set up a specific folder in which to keep your own library installs for testing. This will keep them persistent across sessions. Add something like this to your .Rprofile:

      devlib <- paste('/gscuser/cmiller/usr/lib/R',paste(R.version$major,R.version$minor,sep="."),sep="")
      if (!file.exists(devlib))
      dir.create(devlib)
      x <- .libPaths()
      .libPaths(c(devlib,x))
      rm(x,devlib)
    

This is great for quickly prototyping, but don't forget that if you're sharing code with others, you'll need to create a new container with the proper libraries installed so they can also use it!

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Owner
chrisamiller

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