Update base image to stretch or buster

[nathanweeks]

Would it be non-disruptive to use a newer base image? GNU coreutils df (which is used internally by some bioinformatics utilities, such as MAKER) from Debian jessie is not aware of mount namespaces; rather, it appears hardcoded to derive mount info from /etc/mtab---which isn't created when a biocontainers image is run under Singularity. Consequently, df fails:

$ singularity exec --containall --cleanenv  docker://bitnami/minideb:jessie df
df: cannot read table of mounted file systems: No such file or directory
$ singularity exec --bind /usr/bin/strace --containall --cleanenv docker://bitnami/minideb:jessie strace df 2>&1 | grep '^open'
...
open("/etc/mtab", O_RDONLY|O_CLOEXEC)   = -1 ENOENT (No such file or directory)

df versions from stretch and buster are aware of mount namespaces, and instead read /proc/self/mounts:

$ singularity exec --containall --cleanenv docker://bitnami/minideb:buster df
Filesystem                  1K-blocks    Used Available Use% Mounted on
overlay                         16384      12     16372   1% /
...

[bgruening]

I think this should be fine. Can you create a PR for this please?

[nathanweeks]

Will do!

[epruesse]

How would this impact backwards compatibility with older Linux installations? There are all those clusters that never get updated and still run CentOS 6 ...

[bgruening]

This is only for testing, it's not the build container @epruesse.

[nathanweeks]

@epruesse : It seems Docker Engine is no longer officially supports CentOS 6?

[nathanweeks]

I've noticed that recent Biocontainers images claim a newer os-release:

$ singularity exec csvtk:0.22.0--h9ee0642_1 grep PRETTY_NAME /etc/os-release
PRETTY_NAME="Debian GNU/Linux 10 (buster)"

Are Biocontainers images now built from https://github.com/bioconda/bioconda-containers ? Is this image / repo no longer relevant?

[dpryan79]

I think this was replaced recently. Can you confirm @mbargull ?