FredHutch/ls2_R

Name: ls2_R

Owner: Fred Hutchinson Cancer Research Center

Owner: Fred Hutchinson Cancer Research Center

Description: Our build of R, including many packages

Created: 2017-12-22 19:40:22.0

Updated: 2017-12-22 19:40:22.0

Pushed: 2018-01-09 21:38:46.0

Homepage: null

Size: 18964

Language: null

GitHub Committers

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Other Committers

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README

ls2_R

Our build of R, including many packages our users have requested over the years .

This is an EasyBuild-based build, and pulls the R easyconfig from our easybuild-life-sciences repo on GitHub (is a submodule here).

R package requests should be made in issues on that repo, rather than this one. Issue on this repo should be related to the Dockerfile only.

TODO

[] - add awscli [] - add 'fetch-and-run' for AWS Batch use [] - add Bioconductor packages [] - add unixodbc

Using

The container has a user named neo with UID 500 and home directory /home/neo. All software is installed as that user in ~/.local as EasyBuild does not run as root.

There is no process to run by default, so you will need to run a shell, use the fetch-and-run functionality once added, or extend this container into a new one with your code.

With a shell or script, you will need to activate Lmod and load the R environment module like this:

ce /home/neo/.local/lmod/lmod/init/bash
le use /home/neo/.local/easybuild/modules/all
le load R/3.4.3-foss-2016b-fh2

Build Notes

OS Dependencies:

• unixodbc is still an OS dependency

Version suffix -fh*n* is how we build multiple versions of the same version of software, and should be going away soon.

The build takes a long time.