There seems to be a decent amount of conflicting and out of date information about how to make QIIME2 work for apple silicon. I have not been able to get the current build of QIIIME2 to work on my M1 MacBook via Miniconda. After executing:
CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-osx-conda.yml
I am met with:
EnvironmentNameNotFound: Could not find conda environment: qiime2-amplicon-2024.5
I have seen a few posts about this already but I am curious if there has been any changes in the past few years.
Where is the most up to date guide on how to troubleshoot this?
Thank you!
2 Likes
Hello Tino,
Welcome to the forums!
It looks like already found the current docs for installing Qiime2: Natively installing QIIME 2 — QIIME 2 2024.5.0 documentation
We include support for Apple Silicon M1 osx-arm64 using Rosetta 2, which didn't work for you.
Posting here is the best way to get help!
This error is related to the 2nd line conda activate...CONDA_SUBDIR=osx-64 conda env create... what do you see?
Can you rerun that first line and post the full output? I suspect something went wrong at this first step.
2 Likes
Hi Colin,
thanks for helping me out with this. This is my input and output of the first line of the install code:
(base) s.d.@eduroam-169-233-141-247 ~ % CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-osx-conda.yml
(this is the link to the package 2024.5 but the forum doesn't like new users posting links)
bioconda
conda-forge
defaults
(this is the link to the package 2024.5 but the forum doesn't like new users posting links)
bioconda
conda-forge
defaults
LibMambaUnsatisfiableError: Encountered problems while solving:
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package perl-parent-0.241-pl5321hd8ed1ab_0 is excluded by strict repo priority
package perl-scalar-list-utils-1.63-pl5321h775f41a_0 is excluded by strict repo priority
package argh-0.31.3-pyhd8ed1ab_0 is excluded by strict repo priority
nothing provides r 3.2.2* needed by r-jsonlite-0.9.19-r3.2.2_0
package yq-3.4.3-pyhd8ed1ab_0 requires xmltodict >=0.11.0, but none of the providers can be installed
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package ncbi-datasets-pylib-16.6.1-pyhdfd78af_0 requires urllib3 1.26.*, but none of the providers can be installed
package deblur-1.1.1-pyhdfd78af_0 requires scikit-bio >=0.5.0, but none of the providers can be installed
nothing provides r 3.2.2* needed by r-magrittr-1.5-r3.2.2_0
nothing provides r 3.2.2* needed by r-abind-1.4.3-r3.2.2_0
nothing provides r 3.2.2* needed by r-digest-0.6.9-r3.2.2_0
package bioconductor-phyloseq-1.46.0-r43hdfd78af_0 requires r-ade4 >=1.7-4, but none of the providers can be installed
nothing provides r 3.2.2* needed by r-bit64-0.9_5-r3.2.2_0
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nothing provides __win needed by xopen-2.0.2-pyh7428d3b_1
package emperor-1.0.4-py39h6e9494a_3 is excluded by strict repo priority
nothing provides _python_rc needed by python-3.13.0rc1-h3ec566f_100_cp313
Looks like I am missing a ton of stuff! Thanks for your help.
After some more reading the issue seems to be that I did not input:
conda config --set channel_priority flexible
it seems like this is the solution I needed!
5 Likes
ebolyen
October 3, 2024, 3:45pm
5
It does look like some of the issue was on our end, we've got conda-forge and bioconda backwards in that environment list. So that would explain why you had to drop the channel priority to flexible.@tinoracha !
We should ideally be able to solve with strict in future releases. cc @lizgehret (I think we've fixed this recently already).
5 Likes
system
November 3, 2024, 9:45pm
6
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