build your own singularity image

I was using the tidyverse rocker image on HPC by singularity pull. see my previous post.

Everything was OK until I encountered problems installing jpeg and Cairo R packages. Later, I also had an error installing scRepertoire dependency gsl.

It turns out I have to install debian packages inside the container:

$ apt update && apt install -y --no-install-recommends libjpeg62-turbo-dev zlib1g-dev libpng-dev \
	&& apt install -y --no-install-recommends libx11-dev libcairo2-dev libxt-dev \
	&& apt install -y libgsl-dev 

However, singularity file system is read-only.

You CAN NOT do:

singularity shell rstudio.simg
## and then inside the container
apt install -y --no-install-recommends libjpeg62-turbo-dev zlib1g-dev libpng-dev

Nathan Weeks, our previous docker expert at Harvard FAS informatics told me:

Easiest would be to extend the Docker image, then create a new Singularity image from that.

The followings are the steps I took.

prepare a dockerfile

On my local mac which has docker running prepare a Dockerfile and put it into a folder rocker-jpeg:

FROM rocker/tidyverse:3.6.3
RUN apt update && apt install -y --no-install-recommends libjpeg62-turbo-dev zlib1g-dev libpng-dev \
	&& apt install -y --no-install-recommends libx11-dev libcairo2-dev libxt-dev \
	&& apt install -y libgsl-dev \
 	&& rm -rf /var/lib/apt/lists/*

build the docker image

$ cd rocker-jpeg
## build the extended docker image
$ docker build -t rocker-with-jpeg:3.6.3 .

## push to docker hub
$ docker tag rocker-with-jpeg:3.6.3 crazyhottommy/rocker-with-jpeg:3.6.3

$ docker push crazyhottommy/rocker-with-jpeg:3.6.3

Now, I can install those packages successfully:

$ docker run -it rocker-with-jpeg:3.6.3 bash
$ R

inside R console:

> install.package(c("jpeg", "Cario"))

use the image

I can now either directly singularity pull docker://crazyhottommy/rocker-with-jpeg:3.6.3 to get the singularity image or convert the docker image to singularity image at my local mac:

$ docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp/singularity:/output --privileged -t --rm quay.io/singularity/docker2singularity:v3.6.3 my-rocker-with-jpeg:3.6.3

The resulting singularity image will be in /tmp/singularity.

NOTE: My previous colleague Seth Sahil mentioned that I may want to use the geospacial rocker image since it includes most of the libraries.