Installation 2023.2

Technical Support
1

Hi
I used qiime 1 extensively. Moved away for a while.
I'm trying to install qiime 2 using miniconda using
$ wget https://data.qiime2.org/distro/core/qiime2-2023.2-py38-linux-conda.yml

This runs good.
Next, when I tried to create environment using ..

$ conda env create -n qiime2-2023.2 --file qiime2-2023.2-py38-linux-conda.yml

Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound:

  • q2-vsearch=2023.2.0
  • sepp=4.3.10
  • q2-diversity-lib=2023.2.0
  • q2-taxa=2023.2.0
  • libgfortran-ng=12.2.0
  • q2-feature-table=2023.2.0
  • ld_impl_linux-64=2.40
  • bioconductor-biobase=2.58.0
  • libxkbcommon=1.5.0
    List goes on..

Truly appreciate, if someone can help me to resolve the issue.

Thanks

2

Hello @Venkatakrishna_Jala,

Welcome to the forums! :qiime2:

Did you set up Bioconda?
https://bioconda.github.io/

Once Bioconda is configured, try creating the conda environment for Qiime2 again.
(Many of the Qiime2 packages are in Bioconda, so setting this up is a necessary step.)

3

wget https://data.qiime2.org/distro/core/qiime2-2023.2-py38-linux-conda.yml
conda env create -n qiime2-2023.2 --file qiime2-2023.2-py38-linux-conda.yml

Are these correct commands to work with?

4

I installed miniconda from Bioconda.
I still get the same message. I am missing one small step. Could not figure it.

5

Yes. But first, do this:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

Run those commands. Look for any errors you get and post them here.

Then try installing Qiime2 again.

6

Hi Colin

I did those. But still the same.
Do I have to download QIIME package from somewhere? . May be I am missing that.

(base) C:\Users\jvrao001>conda config --add channels defaults
Warning: 'defaults' already in 'channels' list, moving to the top

(base) C:\Users\jvrao001>conda config --add channels bioconda
Warning: 'bioconda' already in 'channels' list, moving to the top

(base) C:\Users\jvrao001>conda config --add channels conda-forge
Warning: 'conda-forge' already in 'channels' list, moving to the top

(base) C:\Users\jvrao001>conda config --set channel_priority strict

(base) C:\Users\jvrao001>conda env create -n qiime2-2023.2 --file qiime2-2023.2-py38-linux-conda.yml
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound:

  • q2-demux=2023.2.0
7

Hi @Venkatakrishna_Jala,

The problem is that QIIME 2 will only run in a UNIX / LINUX environment. The file paths you show:

are from the Windows command prompt. You need to install the Windows Subsystem for Linux as outlined here.

-Mike

8

Hi Mike

(base) jvrao001@BCC-A92859:~/conda$ conda env create -n qiime2-2023.2 --file qiime2-2023.2-py38-linux-conda.yml
Collecting package metadata (repodata.json): failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/qiime2/label/r2023.2/linux-64/repodata.json
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
'https//conda.anaconda.org/qiime2/label/r2023.2/linux-64'

I'm still getting error.

9

@Venkatakrishna_Jala,

Confirm first that you have a network connection within your linux subsystem, then try running that command again.

10

Thanks Colin Wood. I will check that.
Meanwhile, I am trying to install on MAc.

Venkatakrishnas-MacBook-Pro:~ jvrao001$ conda env create -n qiime2-2023.2 --file qiime2-2023.2-py38-osx-conda.yml
Collecting package metadata (repodata.json): done
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
I'm getting this message.
I acknowledge that I am being naive to install this one.
Truly appreciate your support.
Thank you

11

Hi @Venkatakrishna_Jala, did this work for you on your mac?

12

Hi Gregcaporaso.

No.. it is still giving me ..

(base) dhcp016134:~ jvrao001$ conda env create -n qiime2-2023.2 --file qiime2-2023.2-py38-osx-conda.yml
Collecting package metadata (repodata.json): done
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.

BTW, I installed full Anaconda.
Anaconda3-2023.03-MacOSX-x86_64.pkg
& I did configured to Bioconda.

13

@Venkatakrishna_Jala, there isn't an error message in the output that you provided. It's still possible that the command could complete successfully after the information that was presented. Did you let that run for a while, and if so was any additional output printed to the screen?