Q2-deblur installation problems

User Support
1

Hello,

I just installed QIIME 2 without problems, but I would like to also install q2-deblur. I am having a hard time understanding how to do so. I downloaded the q2-deblur-mater folder and unzip from qiime 2, but then I am stuck. Can anyone helping me, please?

Thank you very much!

2

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
System versions
Python version: 3.5.2
QIIME 2 version: 2017.2.0
q2cli version: 2017.2.0

Installed plugins
alignment 2017.2.0
composition 2017.2.0
dada2 2017.2.0
deblur 2017.2.2
demux 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
  press).

Options:
  --help  Show this message and exit.

Commands:
  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!

3 Likes
3

Thank you so much!!!

It worked perfectly!

Francesca

1 Like
4

Hi @ranocchia,

Just to note, q2-deblur can also be installed into a QIIME2 2017.2 environment via the biocore conda channel:

$ conda install -c biocore q2-deblur
1 Like