pip - Singularity run container - permission denied to run snakemake command

Question

I'm trying to wrap my snakemake pipeline into a singularity container. But I'm not even able to summon snakemake when I want to run my container. During building there is no problem snakemake is here, I can see the snakemake --version print. But when I run my singularity container... I have this issue :

 /.singularity.d/runscript: 3: snakemake: Permission denied

Here is the (minimum) def file to reproduce the error :

BootStrap: debootstrap
OSVersion: focal
MirrorURL: http://us.archive.ubuntu.com/ubuntu/

%runscript
    snakemake --version
%post
    apt-get -y install software-properties-common
    add-apt-repository universe
    apt update
    apt-get -y install python3-pip
    update-alternatives --install /usr/bin/python python /usr/bin/python3.8 2

    python --version
    python -m pip install --user --upgrade cutadapt
    python -m pip install --user --upgrade snakemake

%environment
    PATH="/root/.local/bin/:$PATH"

I tried various things such as (sometimes awkward, but I'm desperate ahah) :

• chmod 777 /root/.local/bin/snakemake
• call snakemake like : /root/.local/bin/snakemake

I'm using singularity version 3.7.0

Could someone help me ? Have a nice day !!

question from:https://stackoverflow.com/questions/66048093/singularity-run-container-permission-denied-to-run-snakemake-command

Answer 1

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