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Re: Squashfs files no longer work with singularity 3.x
From: |
Shane Sturrock |
Subject: |
Re: Squashfs files no longer work with singularity 3.x |
Date: |
Mon, 15 Jul 2019 15:37:22 +1200 |
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 directoryā€¯.
>
> 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