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smdabdoub / kraken-biom

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
MIT License
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biom file not working with Phinch #12

Closed LeonardosMageiros closed 3 years ago

LeonardosMageiros commented 4 years ago

Hi,

have analysed some metagenomic samples using Kraken2 and I would like to visualise my taxonomic profiles using Phinch (http://phinch.org). I used kraken-biom to transform the kraken output to biom format but when I upload the files to Phinch the biom files are not eccepted by the software.

Have you ever faced this issue before? I would appreceate any suggestions

Thank you in advance.

Best Leonardos

casperp commented 4 years ago

Hi Leonardos,

I've faced this issue before. I did fix it it my fork which still has to be merged @smdabdoub. You can try to locally install that fork and use that version. pip install .

heather340 commented 4 years ago

Hi Casper, I'm also having issues using the biom output in Phinch. Can you give me some more detail on how to work with your fork to reflect these fixes...? I'm working in a supercomputer system and just did

pip install git+http://github.com/smdabdoub/kraken-biom.git

to install kraken-biom.

Thanks! Heather

smdabdoub commented 3 years ago

Hi @heather340 and @casperp,

Apologies for taking so long to get on this. I've merged the metadata additions from @casperp, so that should resolve the problem!