From d75b29bd52fdde904864ac8f57ce817a6781561b Mon Sep 17 00:00:00 2001 From: Mark Robinson Date: Sat, 2 May 2020 13:49:22 +0000 Subject: [PATCH] Update README.md --- README.md | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/README.md b/README.md index 4a6b30b..84b775c 100644 --- a/README.md +++ b/README.md @@ -11,3 +11,39 @@ This will start an interactive environment right in your browser. Please see [the documentation](https://renku.readthedocs.io/en/latest/) for more details about Renku. + +## How the images were built + +So, the stack to build the images that work on Renku is a bit convoluted, so here is a description of the layers of layers that are involved. This is mostly left as a Memento to remind myself how I did. If I were to do it again, it would probably be worth organizing it all into one github repo. + +First, we took an image from rocker (I think Carl Boettiger is to thank for these) and I uploaded it to my own dockerhub, like this: + +``` +docker pull rockerdev/rstudio:4.0.0 +docker tag rockerdev/rstudio:4.0.0 markrobinsonuzh/renku:r4.0.0 +docker push markrobinsonuzh/renku:r4.0.0 +``` + +Second, I modified the earlier Bioconductor (many things had changed due to `rockerdev/rstudio:4.0.0` using Ubuntu 20.04) and add a bunch of the bioconductor components (note: my fork of the BioC repo; ), as follows: + +``` +docker build -t bioconductor_docker:4.0.0 https://github.com/markrobinsonuzh/bioconductor_docker.git +docker tag bioconductor_docker:4.0.0 markrobinsonuzh/renku:r4.0.0_bioc +docker push markrobinsonuzh/renku:r4.0.0_bioc +``` + +Next, using Renku's previous docker builds (I'll thank Rok and Emma and Christine here, possibly others!), the tools that are needed under the hood of Renku are added: + +``` +docker build -t markrobinsonuzh/renku:r4.0.0_bioc_renku https://github.com/markrobinsonuzh/renkulab-docker.git\#:docker/bioc +docker push markrobinsonuzh/renku:r4.0.0_bioc_renku +``` + +And then, it's _just_ Renku: + +``` +docker build -t markrobinsonuzh/renku:r4.0.0_bioc_renku_bio334ss2020 https://renkulab.io/gitlab/mark.robinson/bio334_spring2020.git +docker push markrobinsonuzh/renku:r4.0.0_bioc_renku_bio334ss2020 +``` + +This latter one was also built within Renku's builders, so that it can be served up for our course. -- GitLab