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Saskia-Oosterbroek / decona

fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads
MIT License
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bump medaka version supported ? #51

Open arielzn opened 8 months ago

arielzn commented 8 months ago

Hello,

The dependency of medaka=1.1.2 which fixes the dep for tensorflow=2.2.0 (released in 2019....) produces a lot of constraints to install this software with correct GPU support for tensorflow nowadays.

conda-forge packages for tensorflow support the CUDA builds only for tensorflow>=2.4.0 .

So, if i'm not following it wrong, your current approach for installation with a conda environment is producing a CPU only build.

To overcome this issue, could you consider bumping the medaka dependency used ? In order to support more recent tensorflows, it should be to at least medaka=1.6.1

thanks.