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Oefenweb / ansible-r

Ansible role to set up (the latest version of) R in Ubuntu systems
MIT License
42 stars 27 forks source link

bioconductor #7

Closed danhalligan closed 8 years ago

danhalligan commented 8 years ago

Hi, I'm just wondering if you would consider adding support to install R packages via bioconductor. The install process is somewhat different to install.packages():

There is some rough code in one of the comments on this blog post:

If not, would you consider a pull request if I attempted an implementation?

tersmitten commented 8 years ago

That would be a nice addition. Feel free to give it try!

Make sure to have a look at: https://github.com/Oefenweb/ansible-r/blob/master/templates/usr/local/bin/R-install-package.j2 and the remove script in the same folder.

Adding a type property to r_packages could be a solution. What do think?

danhalligan commented 8 years ago

OK great! Ansible is all new to me, so I'm still figuring things out. Currently, I'm looking at adding a separate bioconductor_packages key, but I'm happy to admit this not be best...

danhalligan commented 8 years ago

OK I've forked your repository and made some updates which pass some basic tests. If you like - have a look and check over the code. As I say, I'm new to ansible, so it might be worth checking. I went with your idea of adding a type property though edited the R-install-package.j2 script (as well as adding a test for a bioconductor install).

If your happy, I'll issue a pull request to get this change incorporated.

tersmitten commented 8 years ago

I'll have a look at it soon

danhalligan commented 8 years ago

Just wondering if you'd had a chance to look over this yet -- I think the code is pretty solid so I've issued a pull request

tersmitten commented 8 years ago

Fixed in #9

danhalligan commented 8 years ago

Thanks!