Backwards-compatibility in Singularity (v3 -> v2)

[TimothyOlsson]

Multiple problems with older versions:

• v2 cannot open shub images, which are build in v3 (previously v2). Using Quandenser_pipeline.sh results in:

ERROR : Unknown image format/type: SingulQuand.SIF

• Building with v2 (v2.6.0 tested) results in these errors:

ERROR : Could not write to /usr/local/var/singularity/mnt/final/etc/localtime: Too many levels of symbolic links
ERROR : joinpath() called with NULL path2
ABORT : Retval = 255

So there seems to be multiple levels of errors. First of all, how to distribute the older images and the secondly, making it run

Edit1: Shelling into the image works, but opening the GUI does not. Needs to be further tested on a better VM.

[TimothyOlsson]

ERROR : joinpath() called with NULL path2

Caused by latest change in directory mounts in shell file (https://github.com/statisticalbiotechnology/quandenser-pipeline/blob/master/Quandenser_pipeline.sh#L79)

Causes the directories to ONLY mount latest variable (bad)
Causes empty bind paths (also bad)

Fix ongoing

[TimothyOlsson]

ERROR : joinpath() called with NULL path2

Fixed in fe30040

ERROR: pull is only supported for shub URIs

Fixed in f37da73, now works for 2.X and 3.X

ERROR : Could not write to /usr/local/var/singularity/mnt/final/etc/localtime: Too many levels of symbolic links

Does not affect the pipeline. Seems to disappear in 3.X and only and issue in 2.6.0 (tested). No fix found

ERROR : Unknown image format/type: SingulQuand.SIF
ABORT : Retval = 255

No fix found yet. Seems to work with 2.6.0. Workarounds with building the image from scratch. Perhaps bad image in shub?

[TimothyOlsson]

Seems to be mostly fixed by now. Problem with singhub image also created the problems. I have not yet found anything breaking with the older version.