Open tmozgach opened 6 years ago
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.
Hi, Chris. Can you please report the output of…
brew update
brew install perl cpanm
cpanm PerlIO::gzip
perl -e 'use PerlIO::gzip'
Hi Shaun,
I'm actually trying to do this within a Singularity recipe, but I'm getting the gcc@4.9 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.
Yes, I have MAKER installed at the GSC using Linuxbrew. Can you use gcc
rather than gcc@4.9
?
For Singularity version:
2.4.1
Singularity Recipe: https://github.com/bcgsc/orca/blob/master/Singularity.1
Build the image MANUALLY:
Each user should create an overlay:
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, andSINGULARITY_TMPDIR
for temporary things during build.For example:
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