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snayfach / MicrobeCensus

MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
http://genomebiology.com/2015/16/1/51
GNU General Public License v3.0
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Python2 dependency in conda #20

Closed nigiord closed 6 years ago

nigiord commented 6 years ago

Hi and thank you for this tool,

I've been trying to use MicrobeCensus in a conda environment. The README mentions:

Python version 2 or 3

but the conda package seems to enforce the use of python2.

microbecensus 1.1.1 0

file name : microbecensus-1.1.1-0.tar.bz2 name : microbecensus version : 1.1.1 build string: 0 build number: 0 channel : https://conda.anaconda.org/bioconda/linux-64 size : 20.7 MB arch : x86_64 constrains : () license : GNU General Public License v3 or later (GPLv3+) license_family: GPL3 md5 : d36aac7d4a96c824fd82c073d30db207 platform : linux subdir : linux-64 url : https://conda.anaconda.org/bioconda/linux-64/microbecensus-1.1.1-0.tar.bz2 dependencies: biopython numpy python >=2.7,<3

This is a problem for me since I would like to use MicrobeCensus in a snakemake pipeline, but the packages are in conflict because of this dependency.

UnsatisfiableError: The following specifications were found to be in conflict:
 - microbecensus
 - snakemake

Which one is right? Is conda right to enforce the use of python2 with MicrobeCensus?

Best, Nils

nigiord commented 6 years ago

I made a pull request #21 that allows to install and use microbecensus in Python 3.

This should allow to remove the Python 2 dependency in bioconda.