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saigegit / SAIGE

Development for SAIGE and SAIGE-GENE(+)
GNU General Public License v3.0
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Update dockerfile: Ubuntu 20.04 with system R, OpenBLAS #15

Closed pettyalex closed 2 years ago

pettyalex commented 2 years ago

I noticed that the Dockerfile currently used is using an R version older than you've recommended in the documentation, and also is using Ubuntu 16.04, which has been out of support for a year now.

I reworked the Dockerfile to be based on Ubuntu 20.04, as well as using the Ubuntu-provided R instead of building it locally. It still links against OpenBLAS, I have confirmed in testing.

I also am including another option for a Dockerfile based on the rocker R-langauge docker images. I'm going to test that some locally and see how it compares. It gets us a much newer version of R, but I'm not sure what version of R you are developing SAIGE on, and thought 3.6.1 was safer.

saigegit commented 2 years ago

Thanks so much @pettyalex!! We actually develop SAIGE on the newer R version, e.g. 4.1.2. We will also test the docker file.

pettyalex commented 2 years ago

Whoops! There's a little more cleanup I had intended to do, right here: https://github.com/saigegit/SAIGE/pull/16