Re: Squashfs files no longer work with singularity 3.x

[Shane Sturrock]

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 <address@hidden> 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 address@hidden