From mboxrd@z Thu Jan  1 00:00:00 1970
From: Shane Sturrock <shane.sturrock@realtimegenomics.com>
Subject: Re: Squashfs files no longer work with singularity 3.x
Date: Mon, 15 Jul 2019 15:37:22 +1200
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To: Ricardo Wurmus <rekado@elephly.net>
Cc: help-guix@gnu.org

Thanks Richardo, the --entry-point=3Dbin/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 <rekado@elephly.net> wrote:
>=20
>=20
> Hi Shane,
>=20
>> 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=E2=80=9D.
>=20
> I can reproduce this with singularity version 3.1.0-1.el7.centos.
>=20
>> $ guix pack -f squashfs -S /bin=3Dbin 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
>=20
> This works for me:
>=20
>    image=3D$(guixr pack -f squashfs --entry-point=3Dbin/sh -S /bin=3Dbin=
 samtools bash)
>    singularity exec $image /bin/samtools
>=20
> Hope this helps!
>=20
> --
> Ricardo
>=20

Shane Sturrock, Ph.D
Director of Bio-it
m +64 21 648 466
e shane.sturrock@realtimegenomics.com