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
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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