Missing conda pod5 package

[Salome-Brunon]

Hello,
We have developed a post sequencing QC tool for Nanopore data (ToulligQC) and have incorporated the support for the pod5 format in its latest version.
However, we are unable to package the new version in bioconda due to the lack of a conda module for pod5.
It would be really helpful if a conda pod5 package is created by the nanopore team :)

PS: see below the error I get during the build

Thank you,
Salomé

14:27:25 BIOCONDA INFO (OUT) Traceback (most recent call last):
14:27:25 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/toulligqc_1709734892044/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/toulligqc", line 7, in <module>
14:27:25 BIOCONDA INFO (OUT)     from toulligqc.toulligqc import main
14:27:25 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/toulligqc_1709734892044/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.10/site-packages/toulligqc/toulligqc.py", line 53, in <module>
14:27:25 BIOCONDA INFO (OUT)     from toulligqc import pod5_extractor
14:27:25 BIOCONDA INFO (OUT)   File "/opt/conda/conda-bld/toulligqc_1709734892044/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.10/site-packages/toulligqc/pod5_extractor.py", line 32, in <module>
14:27:25 BIOCONDA INFO (OUT)     import pod5 as p5
14:27:25 BIOCONDA INFO (OUT) ModuleNotFoundError: No module named 'pod5'
14:27:25 BIOCONDA INFO (OUT) Tests failed for toulligqc-2.6-pyhdfd78af_0.tar.bz2 - moving package to /opt/conda/conda-bld/broken
14:27:25 BIOCONDA INFO (OUT) WARNING:conda_build.build:Tests failed for toulligqc-2.6-pyhdfd78af_0.tar.bz2 - moving package to /opt/conda/conda-bld/broken
14:27:25 BIOCONDA INFO (OUT) TESTS FAILED: toulligqc-2.6-pyhdfd78af_0.tar.bz2
14:27:38 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmpfdk2ulr7/build_script.bash:/opt/build_script.bash -v /opt/mambaforge/envs/bioconda/conda-bld/:/opt/host-conda-bld -v /home/vsts/work/1/s/recipes/toulligqc:/opt/recipe -e LANG=C.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7:2.11.1 /bin/bash /opt/build_script.bash

14:27:38 BIOCONDA ERROR BUILD FAILED recipes/toulligqc
14:27:38 BIOCONDA INFO (COMMAND) conda build purge

⠋ running (0:00:00.01)
14:27:40 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
14:27:40 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe recipes/toulligqc

[Mathias-Boulanger]

I am very interested by this feature as well!

I already tried to create conda package recipes for pod5 and its dependencies using conda skeleton pypi pod5 or grayskull pypi pod5 (grayskull) but this is not a smooth build neither.

It will be very useful for the community to have at least all python-based Nanopore tools available in conda-forge or in bioconda. This will help the tools to be used and spread in standardised workflow manager framework (like nf-core)

Thank you for your help.

[simondrue]

I need this as well! :)