Hi @ranocchia, thanks for writing! We haven’t created a conda release (yet!), so installation of
q2-deblur requires a few extra steps.
First, make sure you have QIIME 2 2017.2 installed, as per the instructions here (it sounds like you already have this under control).
Then, run the following
$ source activate qiime2-2017.2
$ conda install --yes -c bioconda VSEARCH==2.0.3 MAFFT==7.221 SortMeRNA==2.0 biom-format
$ conda install --yes -c biocore deblur=1.0.0
$ pip install https://github.com/wasade/q2-deblur/archive/2017.2.2.zip
This should install
q2-deblur dependencies, and then
q2-deblur itself in your conda env. Please note, if you have QIIME 2 installed in an environment other than
qiime2-2017.2, please activate that env, instead!
When you run
qiime info you should see that the
q2-deblur plugin is registered:
$ qiime info
Python version: 3.5.2
QIIME 2 version: 2017.2.0
q2cli version: 2017.2.0
From there, take a peek at the available methods:
$ qiime deblur
Usage: qiime deblur [OPTIONS] COMMAND [ARGS]...
Plugin website: https://github.com/biocore/deblur
Getting user support: https://github.com/biocore/deblur/issues
Citing this plugin: Deblur rapidly resolves single-nucleotide community
sequence patterns. Amnon Amir, Daniel McDonald, Jose A. Navas-Molina,
Evguenia Kopylova, Jamie Morton, Zhenjiang Zech Xu, Eric P. Kightley, Luke
R. Thompson, Embriette R. Hyde, Antonio Gonzalez, Rob Knight. mSystems (in
--help Show this message and exit.
denoise-16S Deblur sequences using a 16S positive filter.
denoise-other Deblur sequences using a user-specified positive filter.
Let us know if you need any additional help with this! Thanks!