search

merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
436 stars 144 forks source link

Going from anvi'o to DESMAN #593

Closed meren closed 5 years ago

meren commented 7 years ago

Going from anvi'o to DESMAN (https://github.com/chrisquince/DESMAN) to deconvolute MAGs with enough variation should be seamless. This may require changes in the DESMAN codebase as well for maximum elegance.

@ozcan, please consider getting some familiarity with DESMAN, so we can sit together and design this the right way :)

vaxherra commented 7 years ago

Hi, Do you have a workflow that takes MAGs produced in Tara Oceans plankton microbiome survey, that uses DESMAN to come up with the final results?

ozcan commented 7 years ago

I have tried DESMAN today and the main problem I noticed is DESMAN uses Python 2 so It seems we can not have a seamless workflow since it is not possible to install both of them in same virtualenv. We still can generate output files DESMAN requires as an input.

chrisquince commented 7 years ago

I would be willing to rewrite into python 3 if it will make integration easier?

ozcan commented 7 years ago

@chrisquince, That would be very good, also I would like to help with that. Initially we switched to Python 3 because snakemake does not supports Python 2 but In DESMAN you have snakemake, how does it work at the moment? Do you guys use virtualenv or just install everything system-wide?

chrisquince commented 7 years ago

Yes it is rather clunky we create two conda environments for Python 2 and 3 and we switch between them within the snakemake. OK lets do it! I actually do not think it will be that hard and I can rationalise some of the code as I go.

vnsriniv commented 6 years ago

Hi all,

I was wondering if there was any update on this? I am starting to work with DESMAN and would love to know if there is an easier way to export anvio binning results to DESMAN.

Thanks! Varun