How to install Qiime2 (in particular Artifact API) with current conda environment? Mac OSX

[jespinoz (Josh Espinoza)]

I want to install qiime2 so I can use Artifact API and make simple wrappers for functions to work with my current workflow. I am having trouble getting qiime2 to install via conda and the https://anaconda.org/qiime2/qiime2 channel.

For example when I run:

conda install -c qiime2/label/r2018.2 qiime2

I get the following error:

(python3) jespinozlt-osx:~ jespinoz$ conda install -c qiime2/label/r2018.2 qiime2
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - qiime2
  - tzlocal

Current channels:

  - https://conda.anaconda.org/qiime2/label/r2018.2/osx-64
  - https://conda.anaconda.org/qiime2/label/r2018.2/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/pro/osx-64
  - https://repo.anaconda.com/pkgs/pro/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Here are my versions:

(python3) jespinozlt-osx:~ jespinoz$ sw_vers
ProductName:	Mac OS X
ProductVersion:	10.11.6
BuildVersion:	15G1217
(python3) jespinozlt-osx:~ jespinoz$ python --version
Python 3.6.4 :: Anaconda, Inc.
(python3) jespinozlt-osx:~ jespinoz$ conda --version
conda 4.5.4

[Nicholas_Bokulich]

Hi @jespinoz,
Have you had a chance to check out our installation guide? Artifact API is included in the basic installation.

To install in an existing conda environment, see this topic:

Installing QIIME2-2018.2 within an existing conda environment

Hello, I am trying to install QIIME2 within an existing conda environment. I use this environment for machine learning, so it already contains important packages. I need to add QIIME2 to this environment, but the installation instructions all require creating a new environment. I tried to install it using the command conda install --file qiime2-2018.2-py35-osx-conda.yml with my machine learning environment activated at the recommendation of @zech_xu , but got the error: could not parse '- q…

I hope that helps!

[jespinoz (Josh Espinoza)]

Hey thanks for the response. I will try it out today. Is it compatible with Python 3.6?

[Nicholas_Bokulich]

@jespinoz

Is it compatible with Python 3.6?

alas, not yet. Looks like you found the open issue tracking this. We will report back here when that issue is closed.

[Nicholas_Bokulich]

I should add: we may just leapfrog on up to 3.7:

Cool things coming to Python 3.7 for QIIME 2

Every now and then I double check that our view type annotations are going to be compatible with future Python versions. Good news! They will be. In fact, it looks like runtime support for type introspection is more or less guaranteed for the near future (including Python 4). There were also a bunch of neat things which I thought others might be interested in: In PEP 557 a new decorator has been added called dataclass which uses the type annotation to dynamically generate a class definition w…

Since it sounds like you want to use :qiime2: with an existing workflow (which I presume depends on python 3.6), I would recommend just installing in a separate (3.5) env following the normal installation instructions, then switch envs when you need to use qiime. A bit inconvenient, but would make your life much easier!

[jespinoz (Josh Espinoza)]

3.7 is out now