Qiime 2.0.6 update / reinstallation using Conda

User Support
1

Dear Qiime2-masters,

I currently have the version 2.0.5 of Qiime installed on my cluster.
I’d like to upgrade it to the just-released newer version.
I tried to activate the environment as root and then:
conda update qiime2
But conda answers that the currently installed version (2.0.5) is up-to-date already.

Many thanks for your support !
Greg

PS: As you may know, I used the following commands to install Qiime2 from scratch:

conda create --name qiime2 -c bioconda -c r bioconductor-dada2 mafft
source activate qiime2

THEN:

conda install -c qiime2 python=3.5 qiime q2cli

conda install matplotlib==1.5.1

conda install -c qiime2 q2-types q2-feature-table

conda install -c qiime2 -c conda-forge q2-diversity q2-emperor emperor=1.0.0beta5

conda install -c biocore fasttree

conda install -c qiime2 q2-demux q2-alignment q2-phylogeny q2-dada2 q2-composition
q2-taxa q2-feature-classifier

2

Hi @Gregory

Looks like you might need to specify the channel in your update command:

conda update -c qiime2 qiime q2cli q2-types q2-feature-table q2-diversity q2-emperor q2-demux q2-alignment q2-phylogeny q2-dada2 q2-composition q2-taxa q2-feature-classifier

Fetching package metadata .........
Solving package specifications: ..........

Package plan for installation in environment /Users/matthew/miniconda3/envs/qiime2.0.5:

The following NEW packages will be INSTALLED:

    tzlocal: 1.3-py35_0   qiime2

The following packages will be UPDATED:

    q2cli:   0.0.5-py35_0 qiime2 --> 0.0.6-py35_0 qiime2
    qiime:   2.0.5-py35_0 qiime2 --> 2.0.6-py35_0 qiime2
    ...

You could also create a new conda environment and install the x.0.6 releases there, too.

Hope that helps!

2 Likes
3

It does help indeed =)

Many thanks @Matthew !

4

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