Installation directly from conda


(John Bradley) #1

The current native QIIME2 installation requires downloading a conda environment file and creating an environment from that file.
https://docs.qiime2.org/2018.6/install/native/#install-qiime-2-within-a-conda-environment

Is it possible to install qiime2 directly from conda?
Something like:
conda install qiime2=2018.6

Thanks.


(Evan Bolyen) #2

Hey @johnbradley!

Kind of, but you need the same channel order in the install file:

https://raw.githubusercontent.com/qiime2/environment-files/master/2018.6/release/qiime2-2018.6-py35-linux-conda.yml

conda install -c <first channel> -c <second channel> -c <etc...> qiime2=2018.6

If you crack that open you’ll see the pieces needed. It turns into a super long command, but if you only* want the framework (qiime2) then that’d be the way to go about it.


(John Bradley) #3

Hey @ebolyen!
Thanks for the quick reply.

I tried your suggestion. It does install the qiime2 python module but not the qiime program and the dependent programs (eg. DADA2). I was trying to use qiime anaconda module with the cwltool software requirements:

Is there a metapackage that wraps up all the modules specified in https://raw.githubusercontent.com/qiime2/environment-files/master/2018.6/release/qiime2-2018.6-py35-linux-conda.yml?
I think I could make it work by translating the above file into a large list of software requirements, but that seems kind of ugly to maintain.

Thanks.


(Nicholas Bokulich) #4

(Evan Bolyen) #5

Hey @johnbradley,

Sorry for the very delayed response :frowning:

There is not, and you’re right. I would avoid hand-crafting that like the plague.

Something we’re hoping to do in the near-future is move the QIIME 2 plugins/framework over to bioconda where we would have good version ranges so that you could reliably install a single plugin with just one command.

In the interum, one of our plans for q2cwl (which I’m pretty sure I showed you in person at BOSC, if not sorry!), is to use a docker container. I haven’t yet had a chance to look to closely at that, but odds are pretty good that we’ll need a different docker container for CWL than our usual one. Or perhaps that one can be updated to play nice with CWL.

If you were interested, I could definitely use some help on that project :wink:


(Evan Bolyen) #6

(John Bradley) #7

@ebolyen Moving to bioconda sound good to me. You did show me an early verison of q2cwl at BOSC. I would be glad to help with that project in my free time.


(Evan Bolyen) #8

I’ve invited you as a collaborator on that repo, welcome! :smiley:

It’s pretty quiet at the moment, but we’re planning on getting that project moving again very soon.


(system) #9

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