Problem in Singularity Container building - Medaka

[Nilad]

I tried to make my own Hybracter Singularity build seems few weeks, with a lot of difficulties (snakemake + python old version = lot of problems)

Right now the core build is :

conda create -y -n hybracter_fix \
        python=3.10 \
        hybracter=0.13.0 \
        snakemake=7.14.0

But i am stuck with Medaka yaml.... (https://github.com/gbouras13/hybracter/blob/main/hybracter/workflow/envs/medaka.yaml) that requires python 3.11

[Tue Jun 23 10:12:16 2026]
Finished job 13.
9 of 23 steps (39%) done
Creating conda environment /opt/conda/envs/hybracter_fix/lib/python3.10/site-packages/hybracter/workflow/envs/pyrodigal.yaml...
Downloading and installing remote packages.
Environment for /opt/conda/envs/hybracter_fix/lib/python3.10/site-packages/hybracter/workflow/envs/pyrodigal.yaml created (location: ../../../../../tmp/hybracter_conda/9367b3c1fa243a361b51afa9332a9846_)
Creating conda environment /opt/conda/envs/hybracter_fix/lib/python3.10/site-packages/hybracter/workflow/envs/dnaapler.yaml...
Downloading and installing remote packages.
Environment for /opt/conda/envs/hybracter_fix/lib/python3.10/site-packages/hybracter/workflow/envs/dnaapler.yaml created (location: ../../../../../tmp/hybracter_conda/aefea18de40d8ff5ff72ccad08d719f3_)
Creating conda environment /opt/conda/envs/hybracter_fix/lib/python3.10/site-packages/hybracter/workflow/envs/medaka.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /opt/conda/envs/hybracter_fix/lib/python3.10/site-packages/hybracter/workflow/envs/medaka.yaml:
Command:
conda env create --quiet --file "/tmp/hybracter_conda/648a2455fc245bde67d6d3221fd723a4_.yaml" --prefix "/tmp/hybracter_conda/648a2455fc245bde67d6d3221fd723a4_"
Output:
Channels:
 - conda-forge
 - bioconda
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... WARNING conda.models.version:get_matcher(564): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 3.11.*, but conda is ignoring the .* and treating it as 3.11
failed

PackagesNotFoundError: The following packages are not available from current channels:

  - python[version='3.10,==3.11.*']

Current channels:

  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/bioconda

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.



[2026:06:23 10:12:39] ERROR: Snakemake failed

[gbouras13]

Hi @Nilad

I am soon about to release an updated version of hybracter.

I have also implemented an automated container build available here (latest will get the latest dev commit) https://quay.io/repository/gbouras13/hybracter?tab=tags - you can find e.g. v0.13.0. I recommend this solution.

George

[Nilad]

Hi @gbouras13,

I have lot of trouble with docker. It's why i make my own Singularity Container directly from Singularity recipe.
I will wait your next release =)