From 945171811e34db08588c95e3611b3964a7792b89 Mon Sep 17 00:00:00 2001
From: Liz Gehret <elizabeth.gehret@gmail.com>
Date: Thu, 24 Oct 2024 18:38:40 -0700
Subject: [PATCH] update envs with py310 & add pathogenome

---
 source/install/index.rst  | 30 +++++++++++++++----
 source/install/native.rst | 62 +++++++++++++++++++++++++++++++--------
 2 files changed, 75 insertions(+), 17 deletions(-)

diff --git a/source/install/index.rst b/source/install/index.rst
index c23c747..044aae4 100644
--- a/source/install/index.rst
+++ b/source/install/index.rst
@@ -39,16 +39,17 @@ option for all cases. In general we recommend the following:
 .. _distributions:
 
 QIIME 2 2024.10 distributions
-----------------------------
+-----------------------------
 
 As of 2024.10, QIIME 2 releases now include the following QIIME 2 distributions that are available for install:
 
 - ``amplicon``
 - ``metagenome``
+- ``pathogenome``
 - ``tiny``
 
 QIIME 2 2024.10 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:
 
@@ -76,7 +77,7 @@ The 2024.10 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 fr
 - ``rescript``
 
 QIIME 2 2024.10 Metagenome Distribution
-......................................
+.......................................
 
 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:
 
@@ -102,14 +103,33 @@ The 2024.10 release of the QIIME 2 Metagenome Distribution includes the QIIME 2
 - ``q2-vsearch``
 - ``rescript``
 
+QIIME 2 2024.10 Pathogenome Distribution
+........................................
+
+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:
+
+- ``q2-amrfinderplus``
+- ``q2-assembly``
+- ``q2-demux``
+- ``q2-feature-classifier``
+- ``q2-feature-table``
+- ``q2-longitudinal``
+- ``q2-quality-control``
+- ``q2-sample-classifier``
+- ``q2-taxa``
+- ``q2-types``
+- ``q2-viromics``
+- ``q2-vizard``
+- ``rescript``
+
 QIIME 2 2024.10 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:
 
 - ``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 Metagenome 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, Metagenome or Pathogenome 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
index 1c435ad..899253f 100644
--- a/source/install/native.rst
+++ b/source/install/native.rst
@@ -62,20 +62,20 @@ QIIME 2 Amplicon Distribution
             </p>
          </div>
          <div id="amplicon-macOS-intel" class="tab-pane fade">
-            <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>
+            <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>
          </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>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
+            <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
    conda activate qiime2-amplicon-2024.10
    conda config --env --set subdir osx-64</pre>
          </div>
          <div id="amplicon-linux" class="tab-pane fade">
-            <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>
+            <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>
          </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>conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py39-linux-conda.yml</pre>
+            <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>
          </div>
       </div>
    </div>
@@ -100,20 +100,58 @@ QIIME 2 Metagenome Distribution
             </p>
          </div>
          <div id="metagenome-macOS-intel" class="tab-pane fade">
-            <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>
+            <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>
          </div>
          <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>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
+            <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
    conda activate qiime2-metagenome-2024.10
    conda config --env --set subdir osx-64</pre>
          </div>
          <div id="metagenome-linux" class="tab-pane fade">
-            <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>
+            <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>
          </div>
          <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>conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py39-linux-conda.yml</pre>
+            <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>
+         </div>
+      </div>
+   </div>
+
+QIIME 2 Pathogenome Distribution
+................................
+
+.. raw:: html
+
+   <div class="tabbed">
+      <ul class="nav nav-tabs">
+         <li class="active"><a data-toggle="tab" href="#pathogenome-instructions">Instructions</a></li>
+         <li><a data-toggle="tab" href="#pathogenome-macOS-intel">macOS (Intel) and OS X</a></li>
+         <li><a data-toggle="tab" href="#pathogenome-macOS-apple-silicon">macOS (Apple Silicon)</a></li>
+         <li><a data-toggle="tab" href="#pathogenome-linux">Linux</a></li>
+         <li><a data-toggle="tab" href="#pathogenome-wsl">Windows (via WSL)</a></li>
+      </ul>
+      <div class="tab-content">
+         <div id="pathogenome-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="pathogenome-macOS-intel" class="tab-pane fade">
+            <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>
+         </div>
+         <div id="pathogenome-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>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
+   conda activate qiime2-pathogenome-2024.10
+   conda config --env --set subdir osx-64</pre>
+         </div>
+         <div id="pathogenome-linux" class="tab-pane fade">
+            <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>
+         </div>
+         <div id="pathogenome-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>conda env create -n qiime2-pathogenome-2024.10 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2024.10-py310-linux-conda.yml</pre>
          </div>
       </div>
    </div>
@@ -138,20 +176,20 @@ QIIME 2 Tiny Distribution
             </p>
          </div>
          <div id="tiny-macOS-intel" class="tab-pane fade">
-            <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>
+            <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>
          </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>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
+            <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
    conda activate qiime2-tiny-2024.10
    conda config --env --set subdir osx-64</pre>
          </div>
          <div id="tiny-linux" class="tab-pane fade">
-            <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>
+            <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>
          </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>conda env create -n qiime2-tiny-2024.10 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py39-linux-conda.yml</pre>
+            <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>
          </div>
       </div>
    </div>