a-ludi / dentist

Close assembly gaps using long-reads at high accuracy.
https://a-ludi.github.io/dentist/
MIT License
47 stars 6 forks source link

Singularity issue #11

Closed DRL closed 3 years ago

DRL commented 3 years ago

Hi,

first time using singularity. Is this supposed to happen or am i supposed to do something else?

$ singularity --debug shell docker://aludi/dentist:latest
DEBUG   [U=2001,P=20764]   persistentPreRun()            Singularity version: 3.6.3
DEBUG   [U=2001,P=20764]   persistentPreRun()            Parsing configuration file /ceph/users/dlaetsch/.conda/envs/singularity/etc/singularity/singularity.conf
DEBUG   [U=2001,P=20764]   handleConfDir()               /ceph/users/dlaetsch/.singularity already exists. Not creating.
DEBUG   [U=2001,P=20764]   getCacheParentDir()           environment variable SINGULARITY_CACHEDIR not set, using default image cache
DEBUG   [U=2001,P=20764]   parseURI()                    Parsing docker://aludi/dentist:latest into reference
FATAL   [U=2001,P=20764]   replaceURIWithImage()         Unable to handle docker://aludi/dentist:latest uri: failed to get checksum for docker://aludi/dentist:latest: Error reading manifest latest in docker.io/aludi/dentist: manifest unknown: manifest unknown

cheers,

dom

DRL commented 3 years ago

For comparison, this command works without problem:

$ singularity --debug run shub://GodloveD/lolcow

a-ludi commented 3 years ago

This is my fault. The correct URL is docker://aludi/dentist:stable. You may also use docker://aludi/dentist:v1.0.1 to get the current release. I will adjust the README accordingly.

I hope this helps. Please close the issue if it works.

DRL commented 3 years ago

Excellent! the URL works, and i could run

$ singularity exec docker://aludi/dentist:stable dentist --version
INFO:    Using cached SIF image
INFO:    Convert SIF file to sandbox...
dentist v1.0.1-1-gc26ba8a-dirty (commit c26ba8afea1c4636f4c63a5e89fed0c1afecc055+dirty)

Copyright © 2018, Arne Ludwig <arne.ludwig@posteo.de>

Subject to the terms of the MIT license, as written in the included LICENSE file
INFO:    Cleaning up image...

Thanks for the quick response!

dom