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To create containers, we use public.docker.itc.griffith.edu.au
Simple "singularity pull" with s3proxy stopped working for docker hubs around Oct 2020. This is due to the changes (limits) docker introduced. To avoid hitting the limits, Griffith team implemented steps to stop direct access through the s3proxy http proxy to the docker hub registry (see https://www.docker.com/blog/understanding-inner-loop-development-and-pull-rates/ for notes)

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singularity shell -B /scratch:/scratch -B /export/home/snumber:/export/home/snumber /export/home/snumber/sw/Containers/container_sandbox

Know the Environment Settings of your Container and the Effect of Using the -e Option

Environment variables set in your current session after sourcing your system startup file, such as .cshrc or .bashrc, or after loading a modulefile, are exported into the container. The only exceptions are PATH and LD_LIBRARY_PATH, which are set differently inside the container compared to the host environment.

The -e or --cleanenv option of the singularity [run, exec, or shell] command lets you clean the environment before running the container. As shown in the table below, adding -e to the singularity exec command retains variables on the left column but removes those on the right column

There may be a difference in behavior when running your container with or without the -e option. For example, if you want to run a graphical application, such as ParaView, within the container, you should add --env DISPLAY=$DISPLAY to the singularity shell command if the -e option is used to start the container:

singularity shell -e --env DISPLAY=$DISPLAY your_container_sandbox

Likely Places to Find Executables or Libraries Inside the Container

For many containers, the default PATH or LD_LIBRARY_PATH might not include paths of executables or libraries needed to run the application of interest. If the container includes MPI libraries, they are commonly installed inside the container in the /usr/local or /usr/local/mpi directories. Other packages are likely installed under the /opt directory of the container. If you still cannot find the executables or libraries and there is no documentation about the container, contact the provider of the container.

Reference

1. http://singularity.lbl.gov/
2. https://www.singularity-hub.org/
3. https://singularityhub.github.io/containers/registry/singularity-hub-registry/
4. https://singularity.lbl.gov/user-guide
5. https://hpc.research.uts.edu.au/software_general/singularity/
6. https://cran.r-project.org/web/views/HighPerformanceComputing.html
7. https://support.pawsey.org.au/documentation/display/US/Running+RStudio+on+Zeus+with+Singularity
8. https://www.katacoda.com/courses/docker
9. https://pawseysc.github.io/containers-bioinformatics-workshop/5.build/index.html
10. https://quay.io/
11. https://pawseysc.github.io/containers-bioinformatics-workshop/3.pipeline/index.html
12. https://ist.mit.edu/xwin32
13. https://pawseysc.github.io/containers-bioinformatics-workshop/1.prep1-ssh/index.html

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