Help with installing songbird

I tried:
(base) Ulis-MacBook-Pro:envs uli$ conda install songbird -c conda-forge

and I have songbird as folder

I did: conda activate qiime2-2020.2
qiime dev refresh-cache
qiime songbird --help
Error: QIIME 2 has no plugin/command named ‘songbird’.

I would really appreciate any help to make “songbird” run under qiime

Please see the installation directions:

Check out the second sentence in this section:

In your QIIME 2 conda environment, you can install Songbird by running:

So based on what you shared above, you are doing the first few steps in the wrong order, you need to activate your qiime2 environment, then install songbird.

Give that a shot and let us know how it goes!

and again I destroyed qiime …
first, I thank thank you for your patience! second, I have to emphasise that I am not an bioinformatician (as you may have noted), third, I do not know what you mean with “In your QIIME 2 conda environment”.
I have the following folder tree: miniconda3 - envs - qiime2-2020.2
In my terminal, I do: conda activate qiime2-2020.2
and doing cd “” I move to my folders
once qiime is working, where do I have to go??? in which folder do I have to go to use the command conda install songbird -c conda-forge; untill now, I only destroyed qiime, re-installed it, destroyed it,…

Hey there,
The “qiime environment” is the installation of qiime running within your machine. Think on your computer as being a box, and you pop down another little box inside it. There you go. That’s the qiime environment.
You activate it by typing conda activate qiime2-2020.2
Apparenttly nothing changes but a “qiime2-2020.2” appearing in the command line.
Now you have to install songbird following the tutorial(step 2 Using Songbird…) and run it.

Hi @rotifer!

No worries - we will get you squared away!

I was sharing a quote from the songbird installation. In the next sentence I reiterated in my own words:

I will demonstrate with commands you could theoretically run:

conda activate qiime2-2020.2
conda install songbird -c conda-forge
qiime dev refresh-cache
qiime info

After running the last command you should see a list of QIIME 2 plugins in your QIIME 2 conda environment, including q2-songbird. You will need to make sure that you have a clean QIIME 2 environment, first.

Lastly, I strongly recommend you read up on conda and miniconda, the working model and terminology is helpful defined and explored there:

In particular, take a look at the links in the “Get Started” section - they should get you situated with the concepts here.

it does not work, I am desperate,I did exactly what you propose:

qiime is dead, therefore:
uli$ conda deactivate
uli$ conda env remove -n qiime2-2020.2
uli$ wget
uli$ conda env create -n qiime2-2020.2 --file qiime2-2020.2-py36-osx-conda.yml
uli$ qiime --help
qiime is alive, therefore
uli$ conda install songbird -c conda-forge

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

Package Plan

environment location: /Users/uli/miniconda3/envs/qiime2-2020.2

added / updated specs:
- songbird
The following NEW packages will be INSTALLED:

songbird conda-forge/osx-64::songbird-1.0.2-py36h9f0ad1d_1

uli$ qiime dev refresh-cache
uli$ qiime info

System versions

Python version: 3.6.7

QIIME 2 release: 2020.2

QIIME 2 version: 2020.2.0

q2cli version: 2020.2.0

Installed plugins

alignment: 2020.2.0

composition: 2020.2.0

cutadapt: 2020.2.0

dada2: 2020.2.0

deblur: 2020.2.0

demux: 2020.2.0

diversity: 2020.2.0

emperor: 2020.2.0

feature-classifier: 2020.2.0

feature-table: 2020.2.0

fragment-insertion: 2020.2.0

gneiss: 2020.2.0

longitudinal: 2020.2.0

metadata: 2020.2.0

phylogeny: 2020.2.0

quality-control: 2020.2.0

quality-filter: 2020.2.0

sample-classifier: 2020.2.0

taxa: 2020.2.0

types: 2020.2.0

vsearch: 2020.2.0

Application config directory


Please review the conda documentation I have shared with you.

This is not what I have proposed, please see my commands above:

You are missing the very first step : conda activate qiime2-2020.2

Also, I am confused about this:

How can QIIME 2 be working, if you haven’t activated your QIIME 2 conda environment?

Please take some time to review the resources I have shared with you.

I did activate and the qiime --help is the check for it, but I will also re-read the documentation