Biom-format issus

[Alak]

Hello,
I tried to install biom-format for metaphlan2. I read that python2.7 or higher should be install, which is my case (2.7). I still receive the message :
Warning! Biom python library not detected!
Exporting to biom format will not work!

Thanks for your help

[George Weingart]

Hi Alak

Can you run biom standalone?

Look at the Path and python path when you run biom standalone and when you invoke metaphlan2

Let me know

Best regards

George Weingart PhD

Huttenhower Lab

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[George Weingart]

Hi Alak,

See my previous email

But, if you can't figure it out:

It is only a warning, so you won't be able to generate output in biom format,  but output is going to be generated in tab format.

If then, still, you want the output in biom format, you can use the biom utilities to convert the tab output generated by metaphlan2 into biom.

Hope this helps

Best regards

George Weingart PhD

Huttenhower Lab

On Tuesday, May 17, 2016, Alak <nat...@gmail.com> wrote:

[Alak]

hello George, thanks for your help!

I am a newbie, I don't even know how to run biom. Could you give more detail how to process?