Thanks Richardo, the --entry-point=bin/sh was the key. I can just call samtools without the leading /bin just fine:
$ singularity --silent exec $image samtools --version samtools 1.9 Using htslib 1.9 Copyright (C) 2018 Genome Research Ltd. Regards, Shane > On 15/07/2019, at 2:26 PM, Ricardo Wurmus <[email protected]> wrote: > > > Hi Shane, > >> However, the most recent updates/installs of Guix produce a file that >> fails with "FATAL: exec /.singularity.d/actions/exec failed: no such >> file or directory”. > > I can reproduce this with singularity version 3.1.0-1.el7.centos. > >> $ guix pack -f squashfs -S /bin=bin samtools >> /gnu/store/7wpn9a4nlpyr0hgzcl65qi8fqmqz6swg-squashfs-pack.gz.squashfs >> $ singularity exec >> /gnu/store/7wpn9a4nlpyr0hgzcl65qi8fqmqz6swg-squashfs-pack.gz.squashfs >> samtools >> WARNING: passwd file doesn't exist in container, not updating >> WARNING: group file doesn't exist in container, not updating >> FATAL: exec /.singularity.d/actions/exec failed: no such file or directory > > This works for me: > > image=$(guixr pack -f squashfs --entry-point=bin/sh -S /bin=bin samtools > bash) > singularity exec $image /bin/samtools > > Hope this helps! > > -- > Ricardo > Shane Sturrock, Ph.D Director of Bio-it m +64 21 648 466 e [email protected]
