From: Ricardo Wurmus <rekado@elephly.net>
To: Shane Sturrock <shane.sturrock@realtimegenomics.com>
Cc: help-guix@gnu.org
Subject: Re: Squashfs files no longer work with singularity 3.x
Date: Mon, 15 Jul 2019 04:26:19 +0200 [thread overview]
Message-ID: <87lfx0hw38.fsf@elephly.net> (raw)
In-Reply-To: <DE8D3C64-1D94-4588-BF14-B321AFDAACAA@realtimegenomics.com>
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
next prev parent reply other threads:[~2019-07-15 2:26 UTC|newest]
Thread overview: 3+ messages / expand[flat|nested] mbox.gz Atom feed top
2019-07-15 0:22 Squashfs files no longer work with singularity 3.x Shane Sturrock
2019-07-15 2:26 ` Ricardo Wurmus [this message]
2019-07-15 3:37 ` Shane Sturrock
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