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 “folder.name” 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.
Cheers,
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:
https://docs.conda.io/projects/conda/en/latest/user-guide/index.html
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 https://data.qiime2.org/distro/core/qiime2-2020.2-py36-osx-conda.yml
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
output:
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
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
/Users/uli/miniconda3/envs/qiime2-2020.2/var/q2cli
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