diann:v1.8.1_cv1 - std::runtime_error

[maff1]

Hi,

I'm using Apptainer (formely Singularity) to build an image, SIF on my local Linux machine to then move it and run on HPC.

SIF file build:

apptainer build diann.sif docker://biocontainers/diann:v1.8.1_cv1

Then running with

apptainer run diann.sif diann -h

Returns terminate called after throwing an instance of 'std::runtime_error' what(): locale::facet::_S_create_c_locale name not valid Aborted (core dumped)

apptainer	distro
1.2.5	Ubuntu 22.04.3 LTS

I also tried to build an image from Dockerfile as suggested in the accepted answer in the thread: https://stackoverflow.com/questions/60314664/how-to-build-singularity-container-from-dockerfile

Any suggestions to sort out this issue?

[maff1]

Quick fix here: https://github.com/BioContainers/containers/issues/554

[ypriverol]

BTW, You don't need to create the singularity container, Biocontainers does it for you @maff1 https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img

[mboudet]

We should probably update the documentation regarding the singularity images..

However, I have the same issue with the diann_v1.8.1_cv1.img file

apptainer run ./diann_v1.8.1_cv1.img -c diann -h
bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
terminate called after throwing an instance of 'std::runtime_error'
  what():  locale::facet::_S_create_c_locale name not valid
Aborted

Since setlocale is running, the issue might be related to the runtime env, and might not occurs everywhere.

[ypriverol]

It may be good to update the documentation, also create in the documentation some kind of Q&A for this kind of questions, that may occur in other containers not only in diann. Feel free to do a PR and I can review it and merge it.

[mboudet]

Sure. I'll look into how to fix this on the Dockerfile-side first.

Something like this (installing the locale package) might work.