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Revert "DEV-BUMP: 2025.4 (#593)"
This reverts commit f5fb4a4.
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‎.github/workflows/ci.yml‎

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- name: install QIIME 2 amplicon distro
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run: |
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envFile=qiime2-amplicon-ubuntu-latest-conda.yml
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wget https://raw.githubusercontent.com/qiime2/distributions/dev/2025.4/amplicon/released/$envFile
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wget https://raw.githubusercontent.com/qiime2/distributions/dev/2024.10/amplicon/released/$envFile
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conda env create -q -p ./test-env --file $envFile
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- name: install conda dependencies

‎source/conf.py‎

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mathjax_path = ('https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2/'
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'MathJax.js?config=TeX-AMS-MML_HTMLorMML')
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html_baseurl = os.environ.get('BASE_URL', 'https://docs.qiime2.org/2025.4/')
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html_baseurl = os.environ.get('BASE_URL', 'https://docs.qiime2.org/2024.10/')

‎source/data-resources.rst‎

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We also provide pre-formatted SILVA reference sequence and taxonomy files here that were processed using `RESCRIPt <https://github.com/bokulich-lab/RESCRIPt>`_. See licensing information below if you use these files.
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- `Silva 138 SSURef NR99 full-length sequences <https://data.qiime2.org/2025.4/common/silva-138-99-seqs.qza>`_ (MD5: ``de8886bb2c059b1e8752255d271f3010``)
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- `Silva 138 SSURef NR99 full-length taxonomy <https://data.qiime2.org/2025.4/common/silva-138-99-tax.qza>`_ (MD5: ``f12d5b78bf4b1519721fe52803581c3d``)
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- `Silva 138 SSURef NR99 515F/806R region sequences <https://data.qiime2.org/2025.4/common/silva-138-99-seqs-515-806.qza>`_ (MD5: ``a914837bc3f8964b156a9653e2420d22``)
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- `Silva 138 SSURef NR99 515F/806R region taxonomy <https://data.qiime2.org/2025.4/common/silva-138-99-tax-515-806.qza>`_ (MD5: ``e2c40ae4c60cbf75e24312bb24652f2c``)
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- `Silva 138 SSURef NR99 full-length sequences <https://data.qiime2.org/2024.10/common/silva-138-99-seqs.qza>`_ (MD5: ``de8886bb2c059b1e8752255d271f3010``)
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- `Silva 138 SSURef NR99 full-length taxonomy <https://data.qiime2.org/2024.10/common/silva-138-99-tax.qza>`_ (MD5: ``f12d5b78bf4b1519721fe52803581c3d``)
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- `Silva 138 SSURef NR99 515F/806R region sequences <https://data.qiime2.org/2024.10/common/silva-138-99-seqs-515-806.qza>`_ (MD5: ``a914837bc3f8964b156a9653e2420d22``)
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- `Silva 138 SSURef NR99 515F/806R region taxonomy <https://data.qiime2.org/2024.10/common/silva-138-99-tax-515-806.qza>`_ (MD5: ``e2c40ae4c60cbf75e24312bb24652f2c``)
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Please cite the following references if you use any of these pre-formatted files:

‎source/install/native.rst‎

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----------------------------------------------
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Once you have Miniconda installed, create a ``conda`` environment and install
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the QIIME 2 2025.4 distribution of your choice within the environment.
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the QIIME 2 2024.10 distribution of your choice within the environment.
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We **highly** recommend creating a *new* environment specifically for the
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QIIME 2 distribution and release being installed, as there are many required
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dependencies that you may not want added to an existing environment.
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You can choose whatever name you'd like for the environment.
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In this example, we'll name the environments ``qiime2-<distro>-2025.4``
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to indicate what QIIME 2 release is installed (i.e. ``2025.4``).
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In this example, we'll name the environments ``qiime2-<distro>-2024.10``
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to indicate what QIIME 2 release is installed (i.e. ``2024.10``).
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QIIME 2 Amplicon Distribution
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.............................
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</p>
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</div>
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<div id="amplicon-macOS-intel" class="tab-pane fade">
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<pre>conda env create -n qiime2-amplicon-2025.4 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2025.4-py310-osx-conda.yml</pre>
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<pre>conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-osx-conda.yml</pre>
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</div>
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<div id="amplicon-macOS-apple-silicon" class="tab-pane fade">
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<p>These instructions are for users with <a href="https://support.apple.com/en-us/HT211814">Apple Silicon</a> chips (M1, M2, etc), and configures the installation of QIIME 2 in <a href="https://developer.apple.com/documentation/apple-silicon/about-the-rosetta-translation-environment">Rosetta 2 emulation mode</a>.</p>
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<pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2025.4 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2025.4-py310-osx-conda.yml
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conda activate qiime2-amplicon-2025.4
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<pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-osx-conda.yml
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conda activate qiime2-amplicon-2024.10
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conda config --env --set subdir osx-64</pre>
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</div>
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<div id="amplicon-linux" class="tab-pane fade">
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<pre>conda env create -n qiime2-amplicon-2025.4 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2025.4-py310-linux-conda.yml</pre>
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<pre>conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-linux-conda.yml</pre>
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</div>
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<div id="amplicon-wsl" class="tab-pane fade">
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<p>These instructions are identical to the Linux instructions and are intended for users of the <a href="https://learn.microsoft.com/en-us/windows/wsl/about">Windows Subsystem for Linux</a>.</p>
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<pre>conda env create -n qiime2-amplicon-2025.4 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2025.4-py310-linux-conda.yml</pre>
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<pre>conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-linux-conda.yml</pre>
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</p>
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</div>
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<div id="metagenome-macOS-intel" class="tab-pane fade">
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<pre>conda env create -n qiime2-metagenome-2025.4 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2025.4-py310-osx-conda.yml</pre>
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<pre>conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-osx-conda.yml</pre>
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</div>
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<div id="metagenome-macOS-apple-silicon" class="tab-pane fade">
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<p>These instructions are for users with <a href="https://support.apple.com/en-us/HT211814">Apple Silicon</a> chips (M1, M2, etc), and configures the installation of QIIME 2 in <a href="https://developer.apple.com/documentation/apple-silicon/about-the-rosetta-translation-environment">Rosetta 2 emulation mode</a>.</p>
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<pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-metagenome-2025.4 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2025.4-py310-osx-conda.yml
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conda activate qiime2-metagenome-2025.4
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<pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-osx-conda.yml
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conda activate qiime2-metagenome-2024.10
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conda config --env --set subdir osx-64</pre>
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</div>
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<div id="metagenome-linux" class="tab-pane fade">
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<pre>conda env create -n qiime2-metagenome-2025.4 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2025.4-py310-linux-conda.yml</pre>
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<pre>conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-linux-conda.yml</pre>
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</div>
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<div id="metagenome-wsl" class="tab-pane fade">
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<p>These instructions are identical to the Linux instructions and are intended for users of the <a href="https://learn.microsoft.com/en-us/windows/wsl/about">Windows Subsystem for Linux</a>.</p>
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<pre>conda env create -n qiime2-metagenome-2025.4 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2025.4-py310-linux-conda.yml</pre>
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<pre>conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-linux-conda.yml</pre>
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</div>
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</div>
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</p>
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</div>
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<div id="pathogenome-macOS-intel" class="tab-pane fade">
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<pre>conda env create -n qiime2-pathogenome-2025.4 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2025.4-py310-osx-conda.yml</pre>
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<pre>conda env create -n qiime2-pathogenome-2024.10 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2024.10-py310-osx-conda.yml</pre>
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</div>
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<div id="pathogenome-macOS-apple-silicon" class="tab-pane fade">
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<p>These instructions are for users with <a href="https://support.apple.com/en-us/HT211814">Apple Silicon</a> chips (M1, M2, etc), and configures the installation of QIIME 2 in <a href="https://developer.apple.com/documentation/apple-silicon/about-the-rosetta-translation-environment">Rosetta 2 emulation mode</a>.</p>
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<pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-pathogenome-2025.4 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2025.4-py310-osx-conda.yml
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conda activate qiime2-pathogenome-2025.4
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<pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-pathogenome-2024.10 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2024.10-py310-osx-conda.yml
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conda activate qiime2-pathogenome-2024.10
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conda config --env --set subdir osx-64</pre>
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</div>
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<div id="pathogenome-linux" class="tab-pane fade">
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<pre>conda env create -n qiime2-pathogenome-2025.4 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2025.4-py310-linux-conda.yml</pre>
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<pre>conda env create -n qiime2-pathogenome-2024.10 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2024.10-py310-linux-conda.yml</pre>
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</div>
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<div id="pathogenome-wsl" class="tab-pane fade">
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<p>These instructions are identical to the Linux instructions and are intended for users of the <a href="https://learn.microsoft.com/en-us/windows/wsl/about">Windows Subsystem for Linux</a>.</p>
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<pre>conda env create -n qiime2-pathogenome-2025.4 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2025.4-py310-linux-conda.yml</pre>
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<pre>conda env create -n qiime2-pathogenome-2024.10 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2024.10-py310-linux-conda.yml</pre>
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</div>
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</p>
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<pre>conda env create -n qiime2-tiny-2025.4 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2025.4-py310-osx-conda.yml</pre>
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<pre>conda env create -n qiime2-tiny-2024.10 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py310-osx-conda.yml</pre>
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</div>
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<div id="tiny-macOS-apple-silicon" class="tab-pane fade">
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<p>These instructions are for users with <a href="https://support.apple.com/en-us/HT211814">Apple Silicon</a> chips (M1, M2, etc), and configures the installation of QIIME 2 in <a href="https://developer.apple.com/documentation/apple-silicon/about-the-rosetta-translation-environment">Rosetta 2 emulation mode</a>.</p>
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<pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-tiny-2025.4 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2025.4-py310-osx-conda.yml
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conda activate qiime2-tiny-2025.4
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<pre>CONDA_SUBDIR=osx-64 conda env create -n qiime2-tiny-2024.10 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py310-osx-conda.yml
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conda activate qiime2-tiny-2024.10
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conda config --env --set subdir osx-64</pre>
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<div id="tiny-linux" class="tab-pane fade">
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<pre>conda env create -n qiime2-tiny-2025.4 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2025.4-py310-linux-conda.yml</pre>
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<pre>conda env create -n qiime2-tiny-2024.10 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py310-linux-conda.yml</pre>
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<div id="tiny-wsl" class="tab-pane fade">
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<p>These instructions are identical to the Linux instructions and are intended for users of the <a href="https://learn.microsoft.com/en-us/windows/wsl/about">Windows Subsystem for Linux</a>.</p>
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<pre>conda env create -n qiime2-tiny-2025.4 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2025.4-py310-linux-conda.yml</pre>
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<pre>conda env create -n qiime2-tiny-2024.10 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py310-linux-conda.yml</pre>
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</div>
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.. command-block::
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conda activate qiime2-<distro>-2025.4
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conda activate qiime2-<distro>-2024.10
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To deactivate an environment, run ``conda deactivate``.
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-----------------------
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If at any point during the analysis the QIIME 2 conda environment is closed
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or deactivated, QIIME 2 2024.10 can be activated (or reactivated) by running
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the following command:
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.. command-block::
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conda activate qiime2-<distro>-2024.10
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‎source/install/virtual/docker.rst‎

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.. command-block::
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3. Confirm the installation
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.. command-block::
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‎source/tutorials/atacama-soils.rst‎

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.. _`atacama demux`:
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Rob Knight, Jack A. Gilbert, Jay Quade, J. Gregory Caporaso, and Raina M.
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Maier. mSystems May 2017, 2 (3) e00195-16; DOI: 10.1128/mSystems.00195-16.
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.. _sample metadata: https://data.qiime2.org/2024.10/tutorials/atacama-soils/sample_metadata

‎source/tutorials/chimera.rst‎

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‎source/tutorials/exporting.rst‎

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‎source/tutorials/feature-classifier.rst‎

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.. download::
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:url: https://data.qiime2.org/2025.4/tutorials/training-feature-classifiers/85_otu_taxonomy.txt
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:url: https://data.qiime2.org/2024.10/tutorials/training-feature-classifiers/85_otu_taxonomy.txt
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:saveas: 85_otu_taxonomy.txt
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Next we import these data into QIIME 2 Artifacts. Since the Greengenes reference taxonomy file (:file:`85_otu_taxonomy.txt`) is a tab-separated (TSV) file without a header, we must specify ``HeaderlessTSVTaxonomyFormat`` as the *source format* since the default *source format* requires a header.
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Finally, we verify that the classifier works by classifying the representative sequences from the `Moving Pictures`_ tutorial and visualizing the resulting taxonomic assignments.
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.. download::
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:url: https://data.qiime2.org/2025.4/tutorials/training-feature-classifiers/rep-seqs.qza
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:url: https://data.qiime2.org/2024.10/tutorials/training-feature-classifiers/rep-seqs.qza
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:saveas: rep-seqs.qza
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.. command-block::

‎source/tutorials/filtering.rst‎

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Download the data we'll use in the tutorial. This includes sample metadata, a feature table, and a distance matrix:
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.. download::
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:url: https://data.qiime2.org/2025.4/tutorials/moving-pictures/sample_metadata.tsv
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:url: https://data.qiime2.org/2024.10/tutorials/moving-pictures/sample_metadata.tsv
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:saveas: sample-metadata.tsv
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.. download::
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:url: https://data.qiime2.org/2025.4/tutorials/filtering/table.qza
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:url: https://data.qiime2.org/2024.10/tutorials/filtering/table.qza
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:saveas: table.qza
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.. download::
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:url: https://data.qiime2.org/2025.4/tutorials/filtering/distance-matrix.qza
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:url: https://data.qiime2.org/2024.10/tutorials/filtering/distance-matrix.qza
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:saveas: distance-matrix.qza
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.. download::
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:url: https://data.qiime2.org/2025.4/tutorials/filtering/taxonomy.qza
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:url: https://data.qiime2.org/2024.10/tutorials/filtering/taxonomy.qza
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.. download::
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:url: https://data.qiime2.org/2025.4/tutorials/filtering/sequences.qza
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:url: https://data.qiime2.org/2024.10/tutorials/filtering/sequences.qza
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:saveas: sequences.qza
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Filtering feature tables

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