Merck / Merck/deepbgc

Installing DeepBGC for pipeline integration

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Description

Hello,

I am developing a genome mining pipeline and would like to include an option for users to submit DeepBGC outputs as inputs to the pipeline. However, I am struggling to install DeepBGC. Can I confirm if it is still maintained and useable on a windows laptop?

Thanks,
Tim

(base) C:\Users\x>conda activate deepbgc

(deepbgc) C:\Users\x>conda config --add channels bioconda

(deepbgc) C:\Users\x>conda config --add channels bioconda
Warning: 'bioconda' already in 'channels' list, moving to the top

(deepbgc) C:\Users\x>conda config --add channels conda-forge

(deepbgc) C:\Users\x>conda install python=3.7 hmmer prodigal
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

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

  - prodigal
  - hmmer

Current channels:

  - https://conda.anaconda.org/conda-forge/win-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/win-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/win-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/win-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/msys2/win-64
  - https://repo.anaconda.com/pkgs/msys2/noarch

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.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the conda setup commands and Windows error output included in the issue, checking how DeepBGC’s Python 3.7 installation depends on hmmer and prodigal. Done means establishing whether Windows is supported and documenting a verified installation path or the specific compatibility limitation.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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