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WatsonLab / MAGpy

Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
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phylophlan 3 #28

Closed geo80 closed 3 years ago

geo80 commented 3 years ago

Hi,

I'm trying to run MAGpy, but I suspect that the setup regarding phylophlan is based on version 2, which is currently unavailable, rather than the newest version 3. Any idea how to modify the file MAGpy to run the new version?

Thanks

mw55309 commented 3 years ago

It would be great to integrate PhyloPhlAn 3 into MAGpy but A LOT has changed, and finding time to do this will be tough.

To run MAGpy without PhyloPhlAn 2 (which is hard to come by), change the file MAGpy:

rule all:
     input: "sourmash_report.csv", "diamond_bin_report_plus.tsv", expand("pfam/{sample}.pfam", sample=IDS), expand("sourmash/{sample}.sm", sample=IDS), expand("diamond_report/bin.{sample}.tsv", sample=IDS), "checkm_plus.txt", "tree/MAGpy/MAGpy.tree.nwk"

Becomes

rule all:
     input: "sourmash_report.csv", "diamond_bin_report_plus.tsv", expand("pfam/{sample}.pfam", sample=IDS), expand("sourmash/{sample}.sm", sample=IDS), expand("diamond_report/bin.{sample}.tsv", sample=IDS), "checkm_plus.txt"
geo80 commented 3 years ago

It would be great to integrate PhyloPhlAn 3 into MAGpy but A LOT has changed, and finding time to do this will be tough.

I realized that! I was trying to confuse it and get some sort of similar results, but it looks like a totally different program.

Thanks. I will change the file as you suggest. Thanks.

Maybe you can update the manual that phylophlan does not work anymore...

Cheers,