Merge pull request #118 from NBISweden/singularity-in-docker

Add info about singularity-in-docker

docs/singularity.md

@@ -424,3 +424,28 @@ so that part of the workflow has already been run and Snakemake will continue
 from that automatically without redoing anything. Once completed you should 
 see a bunch of directories and files generated in your current working 
 directory, including the `results/` directory containing the final HTML report.
+
+## Extra material
+
+A common problem with Singularity is that you can only create local builds if
+you are working on a Linux system, as local builds for MacOS and Windows are
+currently not supported. This means that you might favour using Docker instead
+of Singularity, but what happens when you need to use a HPC cluster such as
+Uppmax? Docker won't work there, as it requires root privileges, so Singularity
+is the only solution. You can only run Singularity images there, however, not
+*build* them...
+
+So, how do you get a Singularity image for use on Uppmax if you can't build it
+either locally or on Uppmax? You might think that using remote builds will solve
+this, but for a lot of cases this won't help. Since most researchers will want
+to work in private Git repositories they can't supply their Conda
+`environment.yml` file to remote builds (which only works for public
+repositories), which means that you'll have to specify packages manually inside
+the container instead.
+
+There is, however, another solution: using Singularity inside Docker. By
+creating a bare-bones, Linux-based Docker image with Singularity you can build
+Singularity images locally on non-Linux operating systems. This can be either
+from Singularity definition files or directly from already existing Docker
+images. You can read more about this at the following
+[GitHub repository](https://github.com/fasterius/singularity-in-docker).