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