MAINT: rename shotgun->metagenome, update plugin list & docker instal…

…l instructions (#582) Co-authored-by: Liz Gehret <[email protected]>
qiime2 · Jun 5, 2024 · f36d546 · f36d546
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diff --git a/source/data-resources.rst b/source/data-resources.rst
@@ -33,10 +33,10 @@ QIIME-compatible SILVA releases (up to release 132), as well as the licensing in
 
 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.
 
-- `Silva 138 SSURef NR99 full-length sequences <https://data.qiime2.org/2024.10/common/silva-138-99-seqs.qza>`_ (MD5: ``de8886bb2c059b1e8752255d271f3010``)
-- `Silva 138 SSURef NR99 full-length taxonomy <https://data.qiime2.org/2024.10/common/silva-138-99-tax.qza>`_ (MD5: ``f12d5b78bf4b1519721fe52803581c3d``)
-- `Silva 138 SSURef NR99 515F/806R region sequences <https://data.qiime2.org/2024.10/common/silva-138-99-seqs-515-806.qza>`_ (MD5: ``a914837bc3f8964b156a9653e2420d22``)
-- `Silva 138 SSURef NR99 515F/806R region taxonomy <https://data.qiime2.org/2024.10/common/silva-138-99-tax-515-806.qza>`_ (MD5: ``e2c40ae4c60cbf75e24312bb24652f2c``)
+- `Silva 138 SSURef NR99 full-length sequences <https://data.qiime2.org/2024.5/common/silva-138-99-seqs.qza>`_ (MD5: ``de8886bb2c059b1e8752255d271f3010``)
+- `Silva 138 SSURef NR99 full-length taxonomy <https://data.qiime2.org/2024.5/common/silva-138-99-tax.qza>`_ (MD5: ``f12d5b78bf4b1519721fe52803581c3d``)
+- `Silva 138 SSURef NR99 515F/806R region sequences <https://data.qiime2.org/2024.5/common/silva-138-99-seqs-515-806.qza>`_ (MD5: ``a914837bc3f8964b156a9653e2420d22``)
+- `Silva 138 SSURef NR99 515F/806R region taxonomy <https://data.qiime2.org/2024.5/common/silva-138-99-tax-515-806.qza>`_ (MD5: ``e2c40ae4c60cbf75e24312bb24652f2c``)
 
 
 Please cite the following references if you use any of these pre-formatted files:
@@ -79,5 +79,5 @@ The following databases are intended for use with q2-fragment-insertion, and
 are constructed directly from the
 `SEPP-Refs project <https://github.com/smirarab/sepp-refs/>`_.
 
-- `Silva 128 SEPP reference database <https://data.qiime2.org/2024.10/common/sepp-refs-silva-128.qza>`_ (MD5: ``7879792a6f42c5325531de9866f5c4de``)
-- `Greengenes 13_8 SEPP reference database <https://data.qiime2.org/2024.10/common/sepp-refs-gg-13-8.qza>`_ (MD5: ``9ed215415b52c362e25cb0a8a46e1076``)
+- `Silva 128 SEPP reference database <https://data.qiime2.org/2024.5/common/sepp-refs-silva-128.qza>`_ (MD5: ``7879792a6f42c5325531de9866f5c4de``)
+- `Greengenes 13_8 SEPP reference database <https://data.qiime2.org/2024.5/common/sepp-refs-gg-13-8.qza>`_ (MD5: ``9ed215415b52c362e25cb0a8a46e1076``)
diff --git a/source/glossary.rst b/source/glossary.rst
@@ -63,7 +63,7 @@ and another geared toward developers. You can find the
      A collection of QIIME 2 plugins that are designed to be installed
      together. These are generally grouped by a theme. For example, the
      Amplicon Distribution provides a collection of plugins for analysis of
-     microbiome amplicon data, while the Shotgun Distribution provides a
+     microbiome amplicon data, while the Metagenome Distribution provides a
      collection of plugins for analysis of microbiome shotgun metagenomics
      data.
 

diff --git a/source/install/index.rst b/source/install/index.rst
@@ -38,19 +38,19 @@ option for all cases. In general we recommend the following:
 
 .. _distributions:
 
-QIIME 2 2024.10 distributions
------------------------------
+QIIME 2 2024.5 distributions
+----------------------------
 
-As of 2024.10, QIIME 2 releases now include the following QIIME 2 distributions that are available for install:
+As of 2024.5, QIIME 2 releases now include the following QIIME 2 distributions that are available for install:
 
 - ``amplicon``
-- ``shotgun``
+- ``metagenome``
 - ``tiny``
 
-QIIME 2 2024.10 Amplicon Distribution
-.....................................
+QIIME 2 2024.5 Amplicon Distribution
+....................................
 
-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:
+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:
 
 - ``q2-alignment``
 - ``q2-composition``
@@ -73,20 +73,24 @@ The 2024.10 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 fr
 - ``q2-taxa``
 - ``q2-types``
 - ``q2-vsearch``
+- ``rescript``
 
-QIIME 2 2024.10 Shotgun Distribution
-....................................
+QIIME 2 2024.5 Metagenome Distribution
+......................................
 
-The 2024.10 release of the QIIME 2 Shotgun Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins:
+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:
 
 - ``q2-assembly``
+- ``q2-composition``
 - ``q2-cutadapt``
 - ``q2-demux``
 - ``q2-diversity``
 - ``q2-diversity-lib``
 - ``q2-emperor``
 - ``q2-feature-classifier``
 - ``q2-feature-table``
+- ``q2-fondue``
+- ``q2-longitudinal``
 - ``q2-metadata``
 - ``q2-moshpit``
 - ``q2-quality-control``
@@ -95,17 +99,17 @@ The 2024.10 release of the QIIME 2 Shotgun Distribution includes the QIIME 2 fra
 - ``q2-sapienns``
 - ``q2-taxa``
 - ``q2-types``
-- ``q2-types-genomics``
+- ``q2-vsearch``
 - ``rescript``
 
-QIIME 2 2024.10 Tiny Distribution
-.................................
+QIIME 2 2024.5 Tiny Distribution
+................................
 
-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:
+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:
 
 - ``q2-types``
 
-The QIIME 2 Tiny Distribution is a minimal QIIME 2 environment that can be used by developers who are in need of a basic development environment, or community plugin users who do not need the entire Amplicon or Shotgun Distributions in their QIIME 2 environment.
+The QIIME 2 Tiny Distribution is a minimal QIIME 2 environment that can be used by developers who are in need of a basic development environment, or community plugin users who do not need the entire Amplicon or Metagenome Distributions in their QIIME 2 environment.
 
 .. note:: The Amplicon Distribution is necessary to run the commands in the :doc:`QIIME 2 tutorials <../tutorials/index>`. If there are additional QIIME 2 plugins or interfaces you would like to install, please consult the relevant package(s) documentation.
 

diff --git a/source/install/native.rst b/source/install/native.rst
@@ -42,13 +42,13 @@ Install QIIME 2 within a ``conda`` environment
 ----------------------------------------------
 
 Once you have Miniconda installed, create a ``conda`` environment and install
-the QIIME 2 2024.10 distribution of your choice within the environment.
+the QIIME 2 2024.5 distribution of your choice within the environment.
 We **highly** recommend creating a *new* environment specifically for the
 QIIME 2 distribution and release being installed, as there are many required
 dependencies that you may not want added to an existing environment.
 You can choose whatever name you'd like for the environment.
-In this example, we'll name the environments ``qiime2-<distro>-2024.10``
-to indicate what QIIME 2 release is installed (i.e. ``2024.10``).
+In this example, we'll name the environments ``qiime2-<distro>-2024.5``
+to indicate what QIIME 2 release is installed (i.e. ``2024.5``).
 
 QIIME 2 Amplicon Distribution
 .............................
@@ -70,82 +70,82 @@ QIIME 2 Amplicon Distribution
             </p>
          </div>
          <div id="amplicon-macOS-intel" class="tab-pane fade">
-            <pre>wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py38-osx-conda.yml
-   conda env create -n qiime2-amplicon-2024.10 --file qiime2-amplicon-2024.10-py38-osx-conda.yml</pre>
+            <pre>wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py38-osx-conda.yml
+   conda env create -n qiime2-amplicon-2024.5 --file qiime2-amplicon-2024.5-py38-osx-conda.yml</pre>
    <span>OPTIONAL CLEANUP</span>
-   <pre>rm qiime2-amplicon-2024.10-py38-osx-conda.yml</pre>
+   <pre>rm qiime2-amplicon-2024.5-py38-osx-conda.yml</pre>
          </div>
          <div id="amplicon-macOS-apple-silicon" class="tab-pane fade">
             <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>
-            <pre>wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py38-osx-conda.yml
-   CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.10 --file qiime2-amplicon-2024.10-py38-osx-conda.yml
-   conda activate qiime2-amplicon-2024.10
+            <pre>wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py38-osx-conda.yml
+   CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.5 --file qiime2-amplicon-2024.5-py38-osx-conda.yml
+   conda activate qiime2-amplicon-2024.5
    conda config --env --set subdir osx-64</pre>
    <span>OPTIONAL CLEANUP</span>
-   <pre>rm qiime2-amplicon-2024.10-py38-osx-conda.yml</pre>
+   <pre>rm qiime2-amplicon-2024.5-py38-osx-conda.yml</pre>
          </div>
          <div id="amplicon-linux" class="tab-pane fade">
-            <pre>wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py38-linux-conda.yml
-   conda env create -n qiime2-amplicon-2024.10 --file qiime2-amplicon-2024.10-py38-linux-conda.yml</pre>
+            <pre>wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py38-linux-conda.yml
+   conda env create -n qiime2-amplicon-2024.5 --file qiime2-amplicon-2024.5-py38-linux-conda.yml</pre>
    <span>OPTIONAL CLEANUP</span>
-   <pre>rm qiime2-amplicon-2024.10-py38-linux-conda.yml</pre>
+   <pre>rm qiime2-amplicon-2024.5-py38-linux-conda.yml</pre>
          </div>
          <div id="amplicon-wsl" class="tab-pane fade">
             <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>
-            <pre>wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py38-linux-conda.yml
-   conda env create -n qiime2-amplicon-2024.10 --file qiime2-amplicon-2024.10-py38-linux-conda.yml</pre>
+            <pre>wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py38-linux-conda.yml
+   conda env create -n qiime2-amplicon-2024.5 --file qiime2-amplicon-2024.5-py38-linux-conda.yml</pre>
    <span>OPTIONAL CLEANUP</span>
-   <pre>rm qiime2-amplicon-2024.10-py38-linux-conda.yml</pre>
+   <pre>rm qiime2-amplicon-2024.5-py38-linux-conda.yml</pre>
          </div>
       </div>
    </div>
 
-QIIME 2 Shotgun Distribution
-............................
+QIIME 2 Metagenome Distribution
+...............................
 
 .. raw:: html
 
    <div class="tabbed">
       <ul class="nav nav-tabs">
-         <li class="active"><a data-toggle="tab" href="#shotgun-instructions">Instructions</a></li>
-         <li><a data-toggle="tab" href="#shotgun-macOS-intel">macOS (Intel) and OS X</a></li>
-         <li><a data-toggle="tab" href="#shotgun-macOS-apple-silicon">macOS (Apple Silicon)</a></li>
-         <li><a data-toggle="tab" href="#shotgun-linux">Linux</a></li>
-         <li><a data-toggle="tab" href="#shotgun-wsl">Windows (via WSL)</a></li>
+         <li class="active"><a data-toggle="tab" href="#metagenome-instructions">Instructions</a></li>
+         <li><a data-toggle="tab" href="#metagenome-macOS-intel">macOS (Intel) and OS X</a></li>
+         <li><a data-toggle="tab" href="#metagenome-macOS-apple-silicon">macOS (Apple Silicon)</a></li>
+         <li><a data-toggle="tab" href="#metagenome-linux">Linux</a></li>
+         <li><a data-toggle="tab" href="#metagenome-wsl">Windows (via WSL)</a></li>
       </ul>
       <div class="tab-content">
-         <div id="shotgun-instructions" class="tab-pane fade in active">
+         <div id="metagenome-instructions" class="tab-pane fade in active">
             <p class="alert alert-warning" style="margin-bottom: 10px;">
               From the above tabs, please choose the installation instructions that are appropriate for your platform.
             </p>
          </div>
-         <div id="shotgun-macOS-intel" class="tab-pane fade">
-            <pre>wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.10-py38-osx-conda.yml
-   conda env create -n qiime2-shotgun-2024.10 --file qiime2-shotgun-2024.10-py38-osx-conda.yml</pre>
+         <div id="metagenome-macOS-intel" class="tab-pane fade">
+            <pre>wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.5-py38-osx-conda.yml
+   conda env create -n qiime2-metagenome-2024.5 --file qiime2-metagenome-2024.5-py38-osx-conda.yml</pre>
    <span>OPTIONAL CLEANUP</span>
-   <pre>rm qiime2-shotgun-2024.10-py38-osx-conda.yml</pre>
+   <pre>rm qiime2-metagenome-2024.5-py38-osx-conda.yml</pre>
          </div>
-         <div id="shotgun-macOS-apple-silicon" class="tab-pane fade">
+         <div id="metagenome-macOS-apple-silicon" class="tab-pane fade">
             <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>
-            <pre>wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.10-py38-osx-conda.yml
-   CONDA_SUBDIR=osx-64 conda env create -n qiime2-shotgun-2024.10 --file qiime2-shotgun-2024.10-py38-osx-conda.yml
-   conda activate qiime2-shotgun-2024.10
+            <pre>wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.5-py38-osx-conda.yml
+   CONDA_SUBDIR=osx-64 conda env create -n qiime2-metagenome-2024.5 --file qiime2-metagenome-2024.5-py38-osx-conda.yml
+   conda activate qiime2-metagenome-2024.5
    conda config --env --set subdir osx-64</pre>
    <span>OPTIONAL CLEANUP</span>
-   <pre>rm qiime2-shotgun-2024.10-py38-osx-conda.yml</pre>
+   <pre>rm qiime2-metagenome-2024.5-py38-osx-conda.yml</pre>
          </div>
-         <div id="shotgun-linux" class="tab-pane fade">
-            <pre>wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.10-py38-linux-conda.yml
-   conda env create -n qiime2-shotgun-2024.10 --file qiime2-shotgun-2024.10-py38-linux-conda.yml</pre>
+         <div id="metagenome-linux" class="tab-pane fade">
+            <pre>wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.5-py38-linux-conda.yml
+   conda env create -n qiime2-metagenome-2024.5 --file qiime2-metagenome-2024.5-py38-linux-conda.yml</pre>
    <span>OPTIONAL CLEANUP</span>
-   <pre>rm qiime2-shotgun-2024.10-py38-linux-conda.yml</pre>
+   <pre>rm qiime2-metagenome-2024.5-py38-linux-conda.yml</pre>
          </div>
-         <div id="shotgun-wsl" class="tab-pane fade">
+         <div id="metagenome-wsl" class="tab-pane fade">
             <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>
-            <pre>wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.10-py38-linux-conda.yml
-   conda env create -n qiime2-shotgun-2024.10 --file qiime2-shotgun-2024.10-py38-linux-conda.yml</pre>
+            <pre>wget https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.5-py38-linux-conda.yml
+   conda env create -n qiime2-metagenome-2024.5 --file qiime2-metagenome-2024.5-py38-linux-conda.yml</pre>
    <span>OPTIONAL CLEANUP</span>
-   <pre>rm qiime2-shotgun-2024.10-py38-linux-conda.yml</pre>
+   <pre>rm qiime2-metagenome-2024.5-py38-linux-conda.yml</pre>
          </div>
       </div>
    </div>
@@ -170,32 +170,32 @@ QIIME 2 Tiny Distribution
             </p>
          </div>
          <div id="tiny-macOS-intel" class="tab-pane fade">
-            <pre>wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py38-osx-conda.yml
-   conda env create -n qiime2-tiny-2024.10 --file qiime2-tiny-2024.10-py38-osx-conda.yml</pre>
+            <pre>wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py38-osx-conda.yml
+   conda env create -n qiime2-tiny-2024.5 --file qiime2-tiny-2024.5-py38-osx-conda.yml</pre>
    <span>OPTIONAL CLEANUP</span>
-   <pre>rm qiime2-tiny-2024.10-py38-osx-conda.yml</pre>
+   <pre>rm qiime2-tiny-2024.5-py38-osx-conda.yml</pre>
          </div>
          <div id="tiny-macOS-apple-silicon" class="tab-pane fade">
             <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>
-            <pre>wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py38-osx-conda.yml
-   CONDA_SUBDIR=osx-64 conda env create -n qiime2-tiny-2024.10 --file qiime2-tiny-2024.10-py38-osx-conda.yml
-   conda activate qiime2-tiny-2024.10
+            <pre>wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py38-osx-conda.yml
+   CONDA_SUBDIR=osx-64 conda env create -n qiime2-tiny-2024.5 --file qiime2-tiny-2024.5-py38-osx-conda.yml
+   conda activate qiime2-tiny-2024.5
    conda config --env --set subdir osx-64</pre>
    <span>OPTIONAL CLEANUP</span>
-   <pre>rm qiime2-tiny-2024.10-py38-osx-conda.yml</pre>
+   <pre>rm qiime2-tiny-2024.5-py38-osx-conda.yml</pre>
          </div>
          <div id="tiny-linux" class="tab-pane fade">
-            <pre>wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py38-linux-conda.yml
-   conda env create -n qiime2-tiny-2024.10 --file qiime2-tiny-2024.10-py38-linux-conda.yml</pre>
+            <pre>wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py38-linux-conda.yml
+   conda env create -n qiime2-tiny-2024.5 --file qiime2-tiny-2024.5-py38-linux-conda.yml</pre>
    <span>OPTIONAL CLEANUP</span>
-   <pre>rm qiime2-tiny-2024.10-py38-linux-conda.yml</pre>
+   <pre>rm qiime2-tiny-2024.5-py38-linux-conda.yml</pre>
          </div>
          <div id="tiny-wsl" class="tab-pane fade">
             <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>
-            <pre>wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py38-linux-conda.yml
-   conda env create -n qiime2-tiny-2024.10 --file qiime2-tiny-2024.10-py38-linux-conda.yml</pre>
+            <pre>wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.5-py38-linux-conda.yml
+   conda env create -n qiime2-tiny-2024.5 --file qiime2-tiny-2024.5-py38-linux-conda.yml</pre>
    <span>OPTIONAL CLEANUP</span>
-   <pre>rm qiime2-tiny-2024.10-py38-linux-conda.yml</pre>
+   <pre>rm qiime2-tiny-2024.5-py38-linux-conda.yml</pre>
          </div>
       </div>
    </div>
@@ -208,7 +208,7 @@ Now that you have a QIIME 2 environment, activate it using the environment's nam
 .. command-block::
    :no-exec:
 
-   conda activate qiime2-<distro>-2024.10
+   conda activate qiime2-<distro>-2024.5
 
 To deactivate an environment, run ``conda deactivate``.
 
@@ -247,13 +247,13 @@ of QIIME 2 and one with the newer version.
 -----------------------
 
 If at any point during the analysis the QIIME 2 conda environment is closed
-or deactivated, QIIME 2 2024.10 can be activated (or reactivated) by running
+or deactivated, QIIME 2 2024.5 can be activated (or reactivated) by running
 the following command:
 
 .. command-block::
    :no-exec:
 
-   conda activate qiime2-<distro>-2024.10
+   conda activate qiime2-<distro>-2024.5
 
 To determine the currently active conda environment, run the following
 command and look for the line that starts with "active environment":