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DEV BUMP 2024.10 TAKE 3 (#592)
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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/2024.5/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/2024.5/')
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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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@@ -33,10 +33,10 @@ QIIME-compatible SILVA releases (up to release 132), as well as the licensing in
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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/2024.5/common/silva-138-99-seqs.qza>`_ (MD5: ``de8886bb2c059b1e8752255d271f3010``)
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- `Silva 138 SSURef NR99 full-length taxonomy <https://data.qiime2.org/2024.5/common/silva-138-99-tax.qza>`_ (MD5: ``f12d5b78bf4b1519721fe52803581c3d``)
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- `Silva 138 SSURef NR99 515F/806R region sequences <https://data.qiime2.org/2024.5/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/2024.5/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/index.rst

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@@ -38,19 +38,19 @@ option for all cases. In general we recommend the following:
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.. _distributions:
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QIIME 2 2024.5 distributions
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QIIME 2 2024.10 distributions
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----------------------------
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As of 2024.5, QIIME 2 releases now include the following QIIME 2 distributions that are available for install:
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As of 2024.10, QIIME 2 releases now include the following QIIME 2 distributions that are available for install:
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- ``amplicon``
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- ``metagenome``
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- ``tiny``
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QIIME 2 2024.5 Amplicon Distribution
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QIIME 2 2024.10 Amplicon Distribution
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....................................
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The 2024.5 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins:
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The 2024.10 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins:
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- ``q2-alignment``
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- ``q2-composition``
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- ``q2-vsearch``
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- ``rescript``
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QIIME 2 2024.5 Metagenome Distribution
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QIIME 2 2024.10 Metagenome Distribution
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......................................
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The 2024.5 release of the QIIME 2 Metagenome Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins:
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The 2024.10 release of the QIIME 2 Metagenome Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins:
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- ``q2-assembly``
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- ``q2-composition``
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- ``q2-vsearch``
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- ``rescript``
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QIIME 2 2024.5 Tiny Distribution
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QIIME 2 2024.10 Tiny Distribution
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................................
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The 2024.5 release of the QIIME 2 Tiny Distribution includes the QIIME 2 framework and ``q2cli`` (a QIIME 2 command-line interface) and the following plugins:
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The 2024.10 release of the QIIME 2 Tiny Distribution includes the QIIME 2 framework and ``q2cli`` (a QIIME 2 command-line interface) and the following plugins:
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- ``q2-types``
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‎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 2024.5 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>-2024.5``
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to indicate what QIIME 2 release is installed (i.e. ``2024.5``).
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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-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-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-py39-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-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-osx-conda.yml
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conda activate qiime2-amplicon-2024.5
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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-py39-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-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-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-py39-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-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-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-py39-linux-conda.yml</pre>
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</div>
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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="metagenome-macOS-intel" class="tab-pane fade">
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<pre>conda env create -n qiime2-metagenome-2024.5 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.5-py39-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-py39-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-2024.5 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.5-py39-osx-conda.yml
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conda activate qiime2-metagenome-2024.5
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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-py39-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-2024.5 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.5-py39-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-py39-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-2024.5 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.5-py39-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-py39-linux-conda.yml</pre>
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</div>
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</div>
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</p>
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<div id="tiny-macOS-intel" class="tab-pane fade">
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<pre>conda env create -n qiime2-tiny-2024.5 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py39-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-py39-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-2024.5 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py39-osx-conda.yml
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conda activate qiime2-tiny-2024.5
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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-py39-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>
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<div id="tiny-linux" class="tab-pane fade">
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<pre>conda env create -n qiime2-tiny-2024.5 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py39-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-py39-linux-conda.yml</pre>
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</div>
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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-2024.5 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py39-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-py39-linux-conda.yml</pre>
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</div>
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</div>
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</div>
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.. command-block::
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:no-exec:
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conda activate qiime2-<distro>-2024.5
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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>-2024.5
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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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docker pull quay.io/qiime2/<distribution>:2024.10
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3. Confirm the installation
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---------------------------
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.. command-block::
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docker run -t -i -v $(pwd):/data quay.io/qiime2/<distribution>:2024.5 qiime
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docker run -t -i -v $(pwd):/data quay.io/qiime2/<distribution>:2024.10 qiime

‎source/tutorials/atacama-soils.rst

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.. download::
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:url: https://data.qiime2.org/2024.5/tutorials/atacama-soils/sample_metadata.tsv
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:url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/sample_metadata.tsv
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.. download::
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:url: https://data.qiime2.org/2024.5/tutorials/atacama-soils/10p/forward.fastq.gz
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:url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/10p/forward.fastq.gz
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:saveas: emp-paired-end-sequences/forward.fastq.gz
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.. download::
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:url: https://data.qiime2.org/2024.5/tutorials/atacama-soils/10p/reverse.fastq.gz
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:url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/10p/reverse.fastq.gz
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.. download::
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:url: https://data.qiime2.org/2024.5/tutorials/atacama-soils/10p/barcodes.fastq.gz
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:url: https://data.qiime2.org/2024.10/tutorials/atacama-soils/10p/barcodes.fastq.gz
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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/2024.5/tutorials/atacama-soils/sample_metadata
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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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Next, download the necessary files:
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:url: https://data.qiime2.org/2024.5/tutorials/chimera/atacama-table.qza
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:url: https://data.qiime2.org/2024.10/tutorials/chimera/atacama-table.qza
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.. download::
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:url: https://data.qiime2.org/2024.5/tutorials/chimera/atacama-rep-seqs.qza
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:url: https://data.qiime2.org/2024.10/tutorials/chimera/atacama-rep-seqs.qza
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‎source/tutorials/exporting.rst

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A ``FeatureTable[Frequency]`` artifact will be exported as a `BIOM v2.1.0 formatted file`_.
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:url: https://data.qiime2.org/2024.10/tutorials/exporting/feature-table.qza
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:url: https://data.qiime2.org/2024.5/tutorials/exporting/unrooted-tree.qza
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:url: https://data.qiime2.org/2024.10/tutorials/exporting/unrooted-tree.qza
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.. command-block::

‎source/tutorials/feature-classifier.rst

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We will also download the representative sequences from the `Moving Pictures`_ tutorial to test our classifier.
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.. download::
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:url: https://data.qiime2.org/2024.5/tutorials/training-feature-classifiers/85_otus.fasta
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:url: https://data.qiime2.org/2024.10/tutorials/training-feature-classifiers/85_otus.fasta
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.. download::
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:url: https://data.qiime2.org/2024.5/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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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/2024.5/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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.. command-block::

‎source/tutorials/filtering.rst

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@@ -19,23 +19,23 @@ First, create a directory to work in and change to that directory.
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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/2024.5/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/2024.5/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/2024.5/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/2024.5/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/2024.5/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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