QIIME 2

The home page for QIIME is here: http://qiime.org This however is for QIIME 1 which will no longer be developed further or supported as of the end of 2017. The QIIME site says:

“We recommend that existing QIIME users begin transitioning from QIIME 1 to QIIME 2 now.”

This install guide here therefore covers the installation of QIIME 2 only. https://qiime2.org

Go to the QIIME 2 homepage at https://qiime2.org then from the menu at the top click on “Docs” to get to the “QIIME 2 user documentation”. From that document click on the link “Natively installing QIIME 2” or go to here: https://docs.qiime2.org/2017.10/install/native/.

This explains that you need to first install Miniconda (this is a small Python distribution) and then under that python distribution install Qiime.

Install Miniconda

See our Python Miniconda install page, then return to here.

Now we are set to install Qiime 2.

Install QIIME 2

Check what is the latest QIIME2. These instructions use a QIIME2 2017 version.

Continue to follow the install notes. Those notes suggest to call your QIIME 2 environment “qiime2-2017.10” based on the QIIME 2 release date. This is a good idea, though you can name it anything you like.

$ conda create -n qiime2-2017.10 --file https://data.qiime2.org/distro/core/qiime2-2017.10-conda-linux-64.txt

qiime2-2017.10 100% |################################| Time: 0:00:00   4.22 MB/s
bioconductor-b 100% |################################| Time: 0:00:08   1.61 MB/s
bioconductor-d 100% |################################| Time: 0:00:01   1.00 MB/s
bioconductor-g 100% |#######
.......
.......
zeromq-4.2.1-1 100% |################################| Time: 0:00:01 455.93 kB/s
zlib-1.2.8-3.t 100% |################################| Time: 0:00:00 215.16 kB/s
$ 

The install has now finished. We can “source” the new QIIME 2 environment to enable it like this:

$ source activate qiime2-2017.10
(qiime2-2017.10) ermdc13 /shared/homes/mlake/$ 

Run Qiime’s help command to check it works:

$ qiime --help

We can also deactivate this environment.

$ source deactivate
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