Issue with multiqc installation with micromamba

[marcodelapierre]

When installing with the newer micromamba-based image, the image does not work.

The installation itself succeeds, but then any multiqc command gives an error of missing the typing_extensions python module. If I manually install it in the image, it then complains about imp, which I am unable to fix.

A quick look at the internet suggests that imp has been deprecated for a while, and hence has probably been removed in newer Pythons. importlib should be used instead.

So I think:

• either we manage to use an older python with micromamba, or
• if only we knew the multiqc developer, who might look into this ... ... @ewels ? 😊

[ewels]

It's because the container switched to Python 3.12. We already released a fix though, so either upgrade MultiQC to v1.17 or pin the Python version to 3.11.

[marcodelapierre]

Thanks Phil.

I thought I had tested 1.17 earlier today with no luck, I will re-run.

Do you know how I can pin the python version with conda/mamba?

PS to reproduce the issue, I go along the lines of:

docker run --rm quay.io/nextflow/rnaseq-nf:v1.2.1 multiqc --version

[marcodelapierre]

Do you know how I can pin the python version with conda/mamba?

Found! ( I wrongly thought was some sort of special dependency )

https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html#conda-yaml-spec-files

[marcodelapierre]

I confirm 1.17 is not enough:

FROM mambaorg/micromamba
MAINTAINER Paolo Di Tommaso <[email protected]>

RUN \
   micromamba install -y -n base -c defaults -c bioconda -c conda-forge \
      salmon=1.10.2 \
      fastqc=0.12.1 \
      multiqc=1.17 \
      procps-ng \
   && micromamba clean -a -y
   #   python=3.11 \

ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
USER root

now pinning python ...

[marcodelapierre]

and neither does this, with multiqc 1.17 and py 3.11:

FROM mambaorg/micromamba
MAINTAINER Paolo Di Tommaso <[email protected]>

RUN \
   micromamba install -y -n base -c defaults -c bioconda -c conda-forge \
      salmon=1.10.2 \
      fastqc=0.12.1 \
      multiqc=1.17 \
      python=3.11 \
      procps-ng \
   && micromamba clean -a -y

ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
USER root

will further test after the kids are in dreamland

[marcodelapierre]

All right, @ewels so we need python 3.11 AND typing_extensions AND importlib_metadata:

FROM mambaorg/micromamba
MAINTAINER Paolo Di Tommaso <[email protected]>

RUN \
   micromamba install -y -n base -c defaults -c bioconda -c conda-forge \
      salmon=1.10.2 \
      fastqc=0.12.1 \
      multiqc=1.17 \
      python=3.11 \
      typing_extensions \
      importlib_metadata \
      procps-ng \
   && micromamba clean -a -y

ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
USER root

[marcodelapierre]

@ewels any idea why Micromamba requires explicit mention of importlib_metadata ?

Without it:

  File "/opt/conda/lib/python3.11/site-packages/multiqc/utils/config.py", line 17, in <module>
    import importlib_metadata
ModuleNotFoundError: No module named 'importlib_metadata'

I am surprised, because the setup.py explicitly mentions it: https://github.com/ewels/MultiQC/blob/master/setup.py#l66

[ewels]

I'm at a conference today + tomorrow, but maybe @vladsavelyev can take a look?

[ewels]

Argh, we didn't update the build requirements on bioconda: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/multiqc/meta.yaml

[ewels]

Should be fixed in conda now 👍🏻