Amplicon Distribution Installation - The missing library

Hello all,

I am trying to install QIIME 2 within miniconda v. 23.10.0 on an iMac Intel Core i5 following the instructions here:
Natively installing QIIME 2 โ€” QIIME 2 2023.9.2 documentation.

I created and activated the new environment env, and installed wget and mamba. When I try to download Amplicon Distribution, it seems to install properly and tells me to activate qiime2-amplicon-2023.9. However, when I do, it tells me that it could not find this conda environment. I'm completely boggled as to where I went wrong and appreciate any and all help!
Interestingly, when I enter conda info --envs, the new environment seems to be there, but it has a blank where the name should be:

base /Users/paul/miniconda3
qenv * /Users/paul/miniconda3/envs/qenv
/Users/paul/miniconda3/envs/qenv/envs/qiime2-amplicon-2023.9

I'm wondering if the fact that qiime2-amplicon-2023.9 is nested in the environment qenv is what is giving me troubles, but no clue how to fix it.
Since its a big text block over the word count, I removed some of the code provided by miniconda during the installation. I would be happy to add it back in in a comment if that is important and no errors or anything odd showed up in this part. I have also bolded the sections where it references the new environment that's giving me troubles. Cheers!

(base) paul@w134-87-041-253 ~ % conda activate qenv
(qenv) paul@w134-87-041-253 ~ % conda install wget
Channels:

  • defaults
    Platform: osx-64
    Collecting package metadata (repodata.json): done
    Solving environment: done

Package Plan

environment location: /Users/paul/miniconda3/envs/qenv

added / updated specs:
- wget

The following NEW packages will be INSTALLED:

ca-certificates pkgs/main/osx-64::ca-certificates-2023.08.22-hecd8cb5_0
libidn2 pkgs/main/osx-64::libidn2-2.3.4-h6c40b1e_0
libunistring pkgs/main/osx-64::libunistring-0.9.10-h9ed2024_0
openssl pkgs/main/osx-64::openssl-3.0.12-hca72f7f_0
wget pkgs/main/osx-64::wget-1.21.4-hf20ceda_1
zlib pkgs/main/osx-64::zlib-1.2.13-h4dc903c_0

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(qenv) paul@w134-87-041-253 ~ % conda install -c conda-forge mamba
Channels:

  • conda-forge
  • defaults
    Platform: osx-64
    Collecting package metadata (repodata.json): done
    Solving environment: done

Package Plan

environment location: /Users/paul/miniconda3/envs/qenv

added / updated specs:
- mamba

The following NEW packages will be INSTALLED:

archspec conda-forge/noarch::archspec-0.2.2-pyhd8ed1ab_0
boltons conda-forge/noarch::boltons-23.0.0-pyhd8ed1ab_0
brotli-python conda-forge/osx-64::brotli-python-1.1.0-py312heafc425_1
bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
c-ares conda-forge/osx-64::c-ares-1.21.0-h10d778d_0
certifi conda-forge/noarch::certifi-2023.7.22-pyhd8ed1ab_0
cffi conda-forge/osx-64::cffi-1.16.0-py312h38bf5a0_0
charset-normalizer conda-forge/noarch::charset-normalizer-3.3.2-pyhd8ed1ab_0
colorama conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0
conda conda-forge/osx-64::conda-23.10.0-py312hb401068_1
conda-libmamba-so~ conda-forge/noarch::conda-libmamba-solver-23.11.0-pyhd8ed1ab_0
conda-package-han~ conda-forge/noarch::conda-package-handling-2.2.0-pyh38be061_0
conda-package-str~ conda-forge/noarch::conda-package-streaming-0.9.0-pyhd8ed1ab_0
fmt conda-forge/osx-64::fmt-10.1.1-h1c7c39f_0
icu conda-forge/osx-64::icu-73.2-hf5e326d_0
idna conda-forge/noarch::idna-3.4-pyhd8ed1ab_0
jsonpatch conda-forge/noarch::jsonpatch-1.33-pyhd8ed1ab_0
jsonpointer conda-forge/osx-64::jsonpointer-2.4-py312hb401068_3
krb5 conda-forge/osx-64::krb5-1.21.2-hb884880_0
libarchive conda-forge/osx-64::libarchive-3.7.2-h0b5dc4a_0
libcurl conda-forge/osx-64::libcurl-8.4.0-h726d00d_0
libcxx conda-forge/osx-64::libcxx-16.0.6-hd57cbcb_0
libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2
libev conda-forge/osx-64::libev-4.33-haf1e3a3_1
libexpat conda-forge/osx-64::libexpat-2.5.0-hf0c8a7f_1
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libiconv conda-forge/osx-64::libiconv-1.17-hac89ed1_0
libmamba conda-forge/osx-64::libmamba-1.5.3-hb976dfd_2
libmambapy conda-forge/osx-64::libmambapy-1.5.3-py312h38108a6_2
libnghttp2 conda-forge/osx-64::libnghttp2-1.58.0-h64cf6d3_0
libsolv conda-forge/osx-64::libsolv-0.7.26-hf4d7fad_0
libsqlite conda-forge/osx-64::libsqlite-3.44.0-h92b6c6a_0
libssh2 conda-forge/osx-64::libssh2-1.11.0-hd019ec5_0
libxml2 conda-forge/osx-64::libxml2-2.11.5-h3346baf_1
libzlib conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5
lz4-c conda-forge/osx-64::lz4-c-1.9.4-hf0c8a7f_0
lzo conda-forge/osx-64::lzo-2.10-haf1e3a3_1000
mamba conda-forge/osx-64::mamba-1.5.3-py312ha12221d_2
ncurses conda-forge/osx-64::ncurses-6.4-h93d8f39_2
packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0
pip conda-forge/noarch::pip-23.3.1-pyhd8ed1ab_0
pluggy conda-forge/noarch::pluggy-1.3.0-pyhd8ed1ab_0
pybind11-abi conda-forge/noarch::pybind11-abi-4-hd8ed1ab_3
pycosat conda-forge/osx-64::pycosat-0.6.6-py312h104f124_0
pycparser conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
pysocks conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6
python conda-forge/osx-64::python-3.12.0-h30d4d87_0_cpython
python_abi conda-forge/osx-64::python_abi-3.12-4_cp312
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
reproc conda-forge/osx-64::reproc-14.2.4.post0-h10d778d_1
reproc-cpp conda-forge/osx-64::reproc-cpp-14.2.4.post0-h93d8f39_1
requests conda-forge/noarch::requests-2.31.0-pyhd8ed1ab_0
ruamel.yaml conda-forge/osx-64::ruamel.yaml-0.18.5-py312h41838bb_0
ruamel.yaml.clib conda-forge/osx-64::ruamel.yaml.clib-0.2.7-py312h104f124_2
setuptools conda-forge/noarch::setuptools-68.2.2-pyhd8ed1ab_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
tqdm conda-forge/noarch::tqdm-4.66.1-pyhd8ed1ab_0
truststore conda-forge/noarch::truststore-0.8.0-pyhd8ed1ab_0
tzdata conda-forge/noarch::tzdata-2023c-h71feb2d_0
urllib3 conda-forge/noarch::urllib3-2.1.0-pyhd8ed1ab_0
wheel conda-forge/noarch::wheel-0.41.3-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
yaml-cpp conda-forge/osx-64::yaml-cpp-0.8.0-he965462_0
zstandard conda-forge/osx-64::zstandard-0.22.0-py312h7a629f7_0
zstd conda-forge/osx-64::zstd-1.5.5-h829000d_0

The following packages will be UPDATED:

openssl pkgs/main::openssl-3.0.12-hca72f7f_0 --> conda-forge::openssl-3.1.4-hd75f5a5_0
zlib pkgs/main::zlib-1.2.13-h4dc903c_0 --> conda-forge::zlib-1.2.13-h8a1eda9_5

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(qenv) paul@w134-87-041-253 ~ % wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2023.9-py38-osx-conda.yml
mamba env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-osx-conda.yml
--2023-11-15 10:45:51-- https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2023.9-py38-osx-conda.yml
Resolving data.qiime2.org (data.qiime2.org)... 54.200.1.12
Connecting to data.qiime2.org (data.qiime2.org)|54.200.1.12|:443... connected.
HTTP request sent, awaiting response... 302 FOUND
Location: https://raw.githubusercontent.com/qiime2/distributions/dev/2023.9/amplicon/released/qiime2-amplicon-macos-latest-conda.yml [following]
--2023-11-15 10:45:51-- https://raw.githubusercontent.com/qiime2/distributions/dev/2023.9/amplicon/released/qiime2-amplicon-macos-latest-conda.yml
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.108.133, 185.199.109.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 12847 (13K) [text/plain]
Saving to: 'qiime2-amplicon-2023.9-py38-osx-conda.yml.3'

qiime2-amplicon-202 100%[===================>] 12.55K --.-KB/s in 0s

2023-11-15 10:45:51 (30.8 MB/s) - 'qiime2-amplicon-2023.9-py38-osx-conda.yml.3' saved [12847/12847]

https://packages.qiime2.org/qiime2/2023.9/amplic.. 0.1s
https://packages.qiime2.org/qiime2/2023.9/amplic.. 0.0s
bioconda/osx-64 (check zst) Checked 0.1s
bioconda/noarch (check zst) Checked 0.1s
pkgs/main/osx-64 (check zst) Checked 0.0s
pkgs/main/noarch (check zst) Checked 0.0s
pkgs/r/osx-64 (check zst) Checked 0.0s
pkgs/r/noarch (check zst) Checked 0.0s
https://packages.qiime2.org/qiime2/2023.9/amplic.. 0.1s
https://packages.qiime2.org/qiime2/2023.9/amplic.. 127.0 B @ 1.6kB/s 0.1s
pkgs/main/noarch 697.6kB @ 2.9MB/s 0.2s
pkgs/r/noarch 2.0MB @ 2.6MB/s 0.5s
pkgs/main/osx-64 5.3MB @ 6.2MB/s 0.8s
pkgs/r/osx-64 694.3kB @ 756.1kB/s 0.1s
bioconda/osx-64 4.3MB @ 4.1MB/s 1.1s
bioconda/noarch 4.7MB @ 3.3MB/s 1.5s
conda-forge/noarch 12.6MB @ 7.1MB/s 1.0s
conda-forge/osx-64 27.3MB @ 10.8MB/s 2.5s

Looking for: ['_r-mutex=1.0.1', 'altair=5.1.2', 'anyio=4.0.0',

__BUNCH OF CODE REMOVED TO SAVE SPACE

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: \
To install TinyTeX with tinytex::install_tinytex() the system must have a functional Perl
installation with a File::Find module. Most end-user systems will already satisfy this
requirement; however, some minimal contexts (e.g., containers) may not. Perl is available
via Conda Forge as the package perl. See TinyTeX needs Perl ยท Issue #419 ยท rstudio/tinytex ยท GitHub

done

# To activate this environment, use
#
# $ conda activate qiime2-amplicon-2023.9

To deactivate an active environment, use

$ conda deactivate

(qenv) paul@w134-87-041-253 ~ % conda activate qiime2-amplicon-2023.9

EnvironmentNameNotFound: Could not find conda environment: qiime2-amplicon-2023.9
You can list all discoverable environments with conda info --envs.

Hi @evepyrenees,

Welcome to the :qiime2: forum!

You're exactly right! Name-based references of conda environments will only work for environments located in one of the directories listed in the envs_dirs configuration option (see conda config --describe envs_dirs). By default, this corresponds to the envs/ subdirectory in the conda installation. If you create an env outside of one of these directories, then you cannot use a name to reference it. Instead, you must activate it by its path - which, in this case would be:

 conda activate /Users/paul/miniconda3/envs/qenv/envs/qiime2-amplicon-2023.9

With that being said, activating by path can be cumbersome - I would actually recommend just removing this environment entirely, and creating a fresh one. Here are the steps I would take for this:

First, remove the nameless environment from your machine.

rm -rf /Users/paul/miniconda3/envs/qenv/envs/qiime2-amplicon-2023.9

Clear any existing cached packages/etc from your conda instance.

conda clean --all

Make sure you don't have an existing conda environment activated before creating a new one (which may be what caused this nested environment location).

conda deactivate

From the location where you'll be downloading the QIIME 2 environment file, you'll want to make sure there are no existing QIIME 2 environment files. You can check with this command:

ls | grep qiime2-*

If there are any existing environment files, go ahead and delete them:

rm qiime2-<env-file-name>.yml

From here, you can follow the standard QIIME 2 installation instructions using conda - this should create a new environment in the correct location with an associated name-based reference.

I hope this helps! Cheers :lizard:

5 Likes

Hi @lizgehret, thank you so much :slight_smile: :slight_smile: :slight_smile: you explained it perfectly and it makes so much sense now

2 Likes

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