Singularity:Overview

[tmozgach]

For Singularity version: 2.4.1

Singularity Recipe: https://github.com/bcgsc/orca/blob/master/Singularity.1

Build the image MANUALLY:

sudo singularity build orca.simg Singularity1

Each user should create an overlay:

singularity image.create --size 3000 overlay.simg 
singularity shell --overlay overlay.simg orca.simg

Problem: During the building image MANUALLY the following error appears: Cannot mkdir: No space left on device during building Explanation: /tmp/ is full Solution: Change cash and tmp directory using environment variables. SINGULARITY_CACHEDIR for persistent things, and SINGULARITY_TMPDIR for temporary things during build.

For example:

SINGULARITY_DISABLE_CACHE=Yes
export SINGULARITY_DISABLE_CACHE
SINGULARITY_CACHEDIR=/home/tmozgacheva/tmp/tmp
export SINGULARITY_CACHEDIR
SINGULARITY_TMPDIR=/home/tmozgacheva/tmp
export SINGULARITY_TMPDIR

AUTOMATED build in Singularity hub (https://singularity-hub.org/) :

Better to set up the manual trigger: https://github.com/singularityhub/singularityhub.github.io/issues/95

Current issue is not solved: https://github.com/singularityhub/singularityhub.github.io/issues/94

[ckeeling]

I notice your singularity recipe says #PerlIO::gzip fails. Have you found a solution for this? This is required for maker, which I have been trying to set up as well, with the same error.

[sjackman]

Hi, Chris. Can you please report the output of…

brew update
brew install perl cpanm
cpanm PerlIO::gzip
perl -e 'use PerlIO::gzip'

[ckeeling]

Hi Shaun,

I'm actually trying to do this within a Singularity recipe, but I'm getting the [email protected] failing before this, so I'm not there yet. Have you had success getting maker set up? I'm trying to do this on cedar.

[sjackman]

Yes, I have MAKER installed at the GSC using Linuxbrew. Can you use gcc rather than [email protected]?