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nanoporetech / megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
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Conda installs megalodon version 2.3.5 instead of 2.4.0. #224

Closed snamburi3 closed 2 years ago

snamburi3 commented 2 years ago

I have installed megalodon with the below commands. Miniforge/Conda installs version 2.3.5 instead of 2.4.0, even-though conda shows version 2.4.0 being installed .

conda config --add channels bioconda
conda install -c bioconda megalodon==2.4.0

Logs: conda list --revisions

    +_libgcc_mutex-0.1 (conda-forge/linux-64)
    +_openmp_mutex-4.5 (conda-forge/linux-64)
    +ca-certificates-2021.10.8 (conda-forge/linux-64)
    +ld_impl_linux-64-2.36.1 (conda-forge/linux-64)
    +libffi-3.4.2 (conda-forge/linux-64)
    +libgcc-ng-11.2.0 (conda-forge/linux-64)
    +libgomp-11.2.0 (conda-forge/linux-64)
    +libnsl-2.0.0 (conda-forge/linux-64)
    +libstdcxx-ng-11.2.0 (conda-forge/linux-64)
    +libzlib-1.2.11 (conda-forge/linux-64)
    +ncurses-6.2 (conda-forge/linux-64)
    +openssl-3.0.0 (conda-forge/linux-64)
    +pip-21.3.1 (conda-forge/noarch)
    +python-3.8.12 (conda-forge/linux-64)
    +python_abi-3.8 (conda-forge/linux-64)
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    +setuptools-59.4.0 (conda-forge/linux-64)
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    +wheel-0.37.0 (conda-forge/noarch)
    +xz-5.2.5 (conda-forge/linux-64)
    +zlib-1.2.11 (conda-forge/linux-64)

2021-12-08 17:02:54  (rev 1)
     openssl  {3.0.0 (conda-forge/linux-64) -> 1.1.1l (conda-forge/linux-64)}
     python  {3.8.12 (conda-forge/linux-64) -> 3.8.12 (conda-forge/linux-64)}
    +brotli-1.0.9 (conda-forge/linux-64)
    +brotli-bin-1.0.9 (conda-forge/linux-64)
    +bzip2-1.0.8 (conda-forge/linux-64)
    +c-ares-1.18.1 (conda-forge/linux-64)
    +cached-property-1.5.2 (conda-forge/noarch)
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    +lz4-c-1.9.3 (conda-forge/linux-64)
    +mappy-2.23 (bioconda/linux-64)
    +matplotlib-base-3.5.0 (conda-forge/linux-64)
    +megalodon-2.4.0 (bioconda/linux-64) 
    +munkres-1.0.7 (bioconda/noarch)
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    +pysam-0.17.0 (bioconda/linux-64)
    +python-dateutil-2.8.2 (conda-forge/noarch)
    +pytz-2021.3 (conda-forge/noarch)
    +scikit-learn-1.0.1 (conda-forge/linux-64)
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    +seaborn-0.11.2 (conda-forge/noarch)
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    +zstd-1.5.0 (conda-forge/linux-64)

2021-12-08 17:09:51  (rev 2)
    +libprotobuf-3.18.1 (conda-forge/linux-64)
    +onnxruntime-1.9.0 (conda-forge/linux-64)
    +protobuf-3.18.1 (conda-forge/linux-64)
    +python-flatbuffers-2.0 (conda-forge/noarch)
    +re2-2021.09.01 (conda-forge/linux-64)

~/bin/miniforge3/envs/ont-py38/bin/megalodon -v

Megalodon version: 2.3.5
marcus1487 commented 2 years ago

The conda release is experimental and not officially supported. I've not seen this issue and am not a conda expert, so I'm not sure I can help too much. Could you post the output of type megalodon on the command line to see if conda is installing megalodon to another location? pip installation is the recommended installation though.