Using sumrep docker spec with singularity

[bcorrie]

Hi All,

We are trying to use the sumrep docker container using singularity. We want to run it on a cluster/hpc machine as a container, but the cluster does not support docker. It only supports singularity as a container platform.

We have used the immcantation docker configuration as a singularity container successfully (converted from the docker container), but we are having problems with sumrep. In particular, we have a permissions problem with the sumrep container. The creation of the singularity container works fine, with some permissions warnings, which are normal in my somewhat limited experience.

The problem is as follows:

• The software inside the container is installed in /sumrep, /partis, etc.
• These directories/files are owned by root
• The permissions for some of the files inside those directories do not have read/execute permissions for "other"
• In singularity, the user does not run as root within the container
• Therefore one can not execute or read these files from within the container

Singularity> ls -l /sumrep/
total 19
-rwxrwx--- 1 root root  366 Sep 30  2019 DESCRIPTION
-rw-rw---- 1 root root 3652 Sep 30  2019 Dockerfile
drwxrwx--- 4 root root  297 Sep 30  2019 Examples
-rwxrwx--- 1 root root   46 Sep 30  2019 NAMESPACE
drwxrwx--- 2 root root  205 Sep 30  2019 R
-rwxrwx--- 1 root root 1257 Sep 30  2019 README.md
drwxrwx--- 3 root root  160 Sep 30  2019 data
drwxrwx--- 2 root root  141 Sep 30  2019 docs
drwxrwx--- 2 root root  116 Sep 30  2019 inst
drwxrwx--- 2 root root 6859 Sep 30  2019 man
-rwxrwx--- 1 root root 6093 Sep 30  2019 partis_env.yml
-rwxrwx--- 1 root root 5793 Sep 30  2019 requirements.txt
-rwxrwx--- 1 root root  267 Sep 30  2019 sumrep.Rproj
drwxrwx--- 3 root root   31 Sep 30  2019 tests

This wouldn't be a problem with docker because you run as root, but in singularity you do not. For example, I can't read /sumrep/DESCRIPTION inside the container. I can't access the data. And I think some of the installation fails as the R packages don't appear to be installed.

Would it be possible for the files to have a +r or +rx permission on them?

Brian