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BU-ISCIII / plasmidID

PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.
https://github.com/BU-ISCIII/plasmidID/wiki
GNU General Public License v3.0
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Unable to copy files to container #9

Closed pedroscampoy closed 5 years ago

pedroscampoy commented 5 years ago

When I run:

sudo singularity build plasmidid.simg Singularity

I get:

WARNING: Authentication token file not found : Only pulls of public images will succeed INFO: Starting build... Getting image source signatures Skipping fetch of repeat blob sha256:8ba884070f611d31cb2c42eddb691319dc9facf5e0ec67672fcfa135181ab3df Copying config sha256:b9a1b1f0b2baaec83946a26d7045e4028f11eccc8b0e5b3514568e56a391beb2 1.05 KiB / 1.05 KiB [======================================================] 0s Writing manifest to image destination Storing signatures INFO: Copying ./scif_app_recipes/ to /opt/ FATAL: container creation failed: unable to copy files to container fs: While copying ./scif_app_recipes/ to /tmp/sbuild-141638742/fs/opt: exit status 1 FATAL: While performing build: while running engine: exit status 255

I have initiated and update submodules: confirmed that files exist. I have tried with several computers and I get the same error message in both.

saramonzon commented 5 years ago

Do you have enough permissions and/or space in /tmp? You can define this build custom Singularity environment variables to any existing path in your PC, by default it uses /tmp. export SINGULARITY_TMPDIR=/custom/path export SINGULARITY_LOCALCACHEDIR=/custom/path More info in singularity docs If this is not the issue, let me know. It works for me in Ubuntu 18 and Centos 6.

saramonzon commented 5 years ago

This is an issue with Singularity version > 3.0, now fixed in Singularity recipe in commit https://github.com/BU-ISCIII/plasmidID/commit/b7c2bfd5e45dd291b362643b13ed16ca9a33fa02

You can see the question asked in Singularity google groups here