TobyBaril / EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline
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perl locale warning in Singularity container #130

Closed mjacksonhill closed 2 months ago

mjacksonhill commented 3 months ago

I'm using the latest singularity container that still uses DFAM 3.7, produced with singularity pull docker://tobybaril/earlgrey:latest. I am executing the analysis on a cluster using slurm.

My run logs are filled with

perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").

This isn't a huge issue but I am wondering if there is anything I can do to rectify it, as this message, repeated over and over, occupies a major portion of my logs. It seems as if I cannot install any packages within the singularity container to fix the issue.

here's the output log from the run I did.

TobyBaril commented 2 months ago

This can be fixed by echoing the following 2 lines to /etc/default/locale inside the container:

echo "LC_ALL=en_US.UTF-8" >> /etc/default/locale
echo "LANG=en_US.UTF-8" >> /etc/default/locale

I'm pushing this to the containers as well, but they might take a bit of time to sync to Docker hub

TobyBaril commented 2 months ago

This is now available on Docker hub for the tags tobybaril:earlgrey_dfam3.7:latest and tobybaril:earlgrey_dfam3.7:v4.4.0