Unable to exec a created singularity image as a non-root user about docker2singularity HOT 5 CLOSED

You shouldn't need to run the docker container as root, but you would need the user added to the Docker group. But there is still the issue with the files permissions.

Could you try rebuilding the container, but commenting these two lines that copy actions and environment scripts? https://github.com/singularityware/docker2singularity/blob/master/docker2singularity.sh#L273

Older versions of Singularity wouldn't provide these, but (I think) it's likely the case that the build will handle it. Let me know if the files exist, and if that resolves the permissions, and I can do a fix.

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Thanks for the quick response @vsoch.

I commented out lines 273 and 274 in the docker2singularity.sh script.

I hadn't noticed that the subsequent commands generate the 10-docker.sh script and copy this into $build_sandbox/.singularity.d/env/ so the first time I ran, the run fails at step 5 with:

(5/10) Setting ENV variables...
cp: can't create '/tmp/testimage.build/.singularity.d/env/10-docker.sh': No such file or directory

I added a line to create this directory after the two commented out lines:

mkdir $build_sandbox/.singularity.d/env; chmod 755 $build_sandbox/.singularity.d/env

The script now runs successfully, creates the testimage.simg file and I can run a terminal in the singularity container without having to be root.

I can also confirm that within the singularity container, /.singularity.d/env contains 6 scripts in addition to 10-docker.sh (i.e. 01-base.sh, 90-environment.sh, etc.)

There are also 5 scripts in the /.singularity.d/actions directory. It looks like these directories are therefore being populated correctly without the copy commands in script.

If you don't mind updating this, that's great, otherwise I'm happy to raise a PR for the changes.

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Woot, good work @jcohen02 I'm so glad that fixed it!

If you have the bandwidth, I'd greatly appreciate a PR to the branch that corresponds with the version you are working with (e.g., https://github.com/singularityware/docker2singularity/tree/v3.3.0). Once that goes through, I'll open another PR for that branch to master.

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Thanks @vsoch, great that this was straightforward to resolve. PR created against v3.3.0.

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Fixed with #68 #69 thanks @jcohen02 !

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