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patrickwest / PhaVa

Identifying phase variation with long reads
MIT License
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dependencies note #1

Closed sconlan closed 1 year ago

sconlan commented 1 year ago

I'm installing now in a conda environment and had a couple of notes for the install.

It took me a minute to figure out einverted is part of emboss

conda install -c bioconda emboss

Not mentioned but phava complained if I didn't install pysam as a dependency

conda install -c bioconda pysam

That along with the mentioned

pip install biopython
conda install -c bioconda minimap2

and it shows the usage screen without errors

patrickwest commented 1 year ago

Thanks for the helpful note, I updated the readme to be more clear on the dependencies