suggested dockerfile amendments for singularity

[che25]

There are two issues that I managed to sort out myself, but it would be helpful if you could adopt the changes. The issues only occur with singularity, not with docker itself.

• main script is not found unless started explicitly in the root director /
• R script requires LC_ALL = C

ENV LC_ALL C ENTRYPOINT bash /run_workflow.sh

[adelabriere]

Thanks you very much for the reports, I will include these fix. It is surprising that I never had any of these issues on our cluster. Could it be possible that you exports your own environment variables and they override the default in the container singularity ? It still need a fix for sure.

If not what is your system ?

[che25]

It’s a linux hpc cluster.

@.*** ~]$ uname -a Linux r2d2 4.18.0-305.12.1.el8_4.x86_64 #1 SMP Wed Aug 11 01:59:55 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

@.*** ~]$ singularity --version singularity version 3.8.1-1.el8

Best

C

On 31 Aug 2021, at 18:21, Alexis Delabriere @.***> wrote:

Thanks a lot for the reports, I will include these fix. It is surprising that I never had any of this issues on our cluster, which is surprising. Could it be possible that you exports your own environment variables and they override the default in singularity ? It still need a fix for sure.

If not what is your system ?

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[adelabriere]

@che25 Very sorry for the delay, the requested changed have been made.