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WatsonLab / MAGpy

Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
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install phylophlan #24

Closed chen318liang closed 3 years ago

chen318liang commented 4 years ago

The web of https://bitbucket.org/nsegata/phylophlan is seems not available now? Is there other ways to get phylophlan2?

dsarov commented 3 years ago

I'm hitting the same error. I've tried installing with conda (conda install -c bioconda phylophlan) but the python version is incompatible. Inclusion in the initial install of the environment (i.e. in the yaml file), might fix this issue?

mw55309 commented 3 years ago

Hi @dsarov MAGpy works with PhyloPhlAN 2 only - PhyloPhlAN 3 (via conda) is an entirely different piece of software and we haven't figure out how to integrate it yet

To run MAGpy without PhyloPhlAN, remove , "tree/MAGpy/MAGpy.tree.nwk" from rule all

dsarov commented 3 years ago

Thanks! @mw55309

mw55309 commented 3 years ago

Hey

There is a new release today that fixes a lot of sourmash and phylophlan bugs

Please test it!

Cheers Mick