checkqc: InterOp is not installed in docker image

[matrulda]

Regarding checkqc version: 4.0.1 build 0

Hi!

I need some help with troubleshooting the docker image created for checkqc. When trying to use it, I get the following error when trying to process a run folder:

  Traceback (most recent call last):
  File "/usr/local/bin/checkqc", line 10, in <module>
    sys.exit(start())
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/usr/local/lib/python3.10/site-packages/checkQC/app.py", line 41, in start
    app.run()
  File "/usr/local/lib/python3.10/site-packages/checkQC/app.py", line 104, in run
    reports = self.configure_and_run()
  File "/usr/local/lib/python3.10/site-packages/checkQC/app.py", line 87, in configure_and_run
    reports = qc_engine.run()
  File "/usr/local/lib/python3.10/site-packages/checkQC/qc_engine.py", line 56, in run
    self._create_handlers()
  File "/usr/local/lib/python3.10/site-packages/checkQC/qc_engine.py", line 69, in _create_handlers
    create_subclass_instance(clazz_config["name"], clazz_config))
  File "/usr/local/lib/python3.10/site-packages/checkQC/handlers/qc_handler_factory.py", line 32, in create_subclass_instance
    importlib.import_module(modname)
  File "/usr/local/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 688, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 883, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/usr/local/lib/python3.10/site-packages/checkQC/handlers/error_rate_handler.py", line 3, in <module>
    from checkQC.parsers.interop_parser import InteropParser
  File "/usr/local/lib/python3.10/site-packages/checkQC/parsers/interop_parser.py", line 4, in <module>
    from interop import py_interop_run_metrics, py_interop_run, py_interop_summary
ModuleNotFoundError: No module named 'interop'

It looks like the InterOp module is not installed. The conda package and singularity image does not have this issue. I am not able get the bioconda-utils to work (bioconda/bioconda-utils#929) so I'm not sure what happens during the build process for the docker image. I would very much appreciate help with this since it is blocking me from completing the CheckQC module for nf-core: nf-core/modules#4158

Do you have any ideas, @cbrueffer?

Steps to reproduce error:

docker pull quay.io/biocontainers/checkqc:4.0.1--pyhdfd78af_0
git clone https://github.com/Molmed/checkQC.git
docker run -v $PWD:$PWD <docker image ID> checkqc $PWD/checkQC/tests/resources/170726_D00118_0303_BCB1TVANXX/

[matrulda]

I think this issue is caused by the way illumina-interop is installed:

bioconda-recipes/recipes/illumina-interop/meta.yaml

Line 5 in c6d4da0

name: illumina-interop

CheckQC need the interop module to be available at /usr/local/lib/python3.10/site-packages/, this could be achieved by installing the interop package with pip.

[matrulda]

As a sidenote: This also affects the singularity and conda build. I just didn't notice since singularity was "clever" enough to import the module from my local machine:

singularity shell checkqc\:4.0.1--pyhdfd78af_0
Singularity> python
Python 3.10.13 | packaged by conda-forge | (main, Dec 23 2023, 15:36:39) [GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import interop
>>> print(interop.__file__)
/home/matilda/.local/lib/python3.10/site-packages/interop/__init__.py

[mahesh-panchal]

Ah, seems you got there.
Add export PYTHONNOUSERSITE=1 when testing so it doesn't pick up local modules.
This is in the nf-core configs too: https://github.com/nf-core/tools/blob/9eac5e9b33a4b86a5228e950a8c8fd16765f4a85/nf_core/pipeline-template/nextflow.config#L211

[matrulda]

Hmm, I think I'm gonna need help with this one. The interop package on PyPI does not have a source distribution, so I'm unsure how to properly set this up.

@alneberg Made me aware of the fact that conda skeleton pypi checkqc actually generates a template that uses interop instead of illumina-interop on this line:

bioconda-recipes/recipes/checkqc/meta.yaml

Line 30 in 0e11306

- illumina-interop >=1.2.4

so perhaps that is the issue after all.

[cbrueffer]

Hi @matrulda, you're right, illumina-interop doesn't install the Python bindings. I looked at this last year (#40431), but didn't finish it up. I'll look into this later today. The template using the name interop is just because that's the name of the Python module; the recipe name is irrelevant for the problem.

[matrulda]

Ah great, thank you very much @cbrueffer 👍