If I pull a docker image with singularity 2.5.2 it runs fine with the 3.1.1 exec:
$ /software/singularity-3.1.1/bin/singularity exec dockstore-cgpwxs_singularity_bug_report_pull_2.5.2.simg samtools view
Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]
...
If I then pull the same image with 3.1.1 and attempt to run it I get problems loading shared libraries, these are ones being used within the container (not by singularity itself as in #3027):
$ /software/singularity-3.1.1/bin/singularity exec dockstore-cgpwxs_singularity_bug_report_pull_3.1.1.simg samtools view
samtools: error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory
On the container pulled with 3.1.1 I've checked the files indicated as being a problem:
$ /software/singularity-3.1.1/bin/singularity exec dockstore-cgpwxs_singularity_bug_report_pull_3.1.1.simg ls -l /opt/wtsi-cgp/lib/
total 8613
-rwxr-xr-x 1 root root 415532 Apr 16 10:33 libBigWig.a
-rwxr-xr-x 1 root root 240712 Apr 16 10:33 libBigWig.so
-rw-r--r-- 1 root root 4950682 Apr 16 10:33 libhts.a
lrwxrwxrwx 1 root root 13 Apr 16 10:33 libhts.so -> libhts.so.1.9
-rw-r--r-- 1 root root 3211128 Apr 16 10:33 libhts.so.1.9
lrwxrwxrwx 1 root root 13 Apr 16 10:33 libhts.so.2 -> libhts.so.1.9
drwxrwxr-x 63 root root 1186 Apr 16 07:31 perl5
drwxr-xr-x 2 root root 32 Apr 15 08:08 pkgconfig
This is an exact match to the same folder when pulled with 2.5.2.
I'd expect the image pulled with 3.1.1 and executed with 3.1.1 to function better than one pulled with 2.5.2.
Linked GitHub issue
