Can't run snakemake (or cutadapt) inside a singularity container - Permission denied

[Elsa Claude]

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 !!

[Kandes, Martin]

Hi Elsa,

You should remove the --user flags on your pip installs. When building the container, it is built as root. So applying --user will install the packages in the root user's .local python package library. But when you run the container on some system, you will not be running the container as the root user. Removing the --user flags will install the packages within the container such that any user can run the container and use them.

Marty

---

From: Elsa Claude <elsacl...@gmail.com>
Sent: Thursday, February 4, 2021 7:20 AM
To: singularity <singu...@lbl.gov>
Subject: [Singularity] Can't run snakemake (or cutadapt) inside a singularity container - Permission denied

 

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[Elsa Claude]

Great !!

It works perfectly now !

Thanks Marty, have a nice day :)