Installation 2023.2 – Technical Support

Hi
I used qiime 1 extensively. Moved away for a while.
I’m trying to install qiime 2 using miniconda using
$ wget 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


Hello @Venkatakrishna_Jala,

Welcome to the forums! :qiime2:

Did you set up Bioconda?
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.)



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wget 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?

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

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.



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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:

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



1 Like

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 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.

@Venkatakrishna_Jala,

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

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

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

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.

Read more here: Source link