From 82366ee4c94eb863c16e3726f979e60b1e969c63 Mon Sep 17 00:00:00 2001
From: Liz Gehret <54517601+lizgehret@users.noreply.github.com>
Date: Thu, 27 Jun 2024 14:44:01 -0700
Subject: [PATCH] MAINT: sepp-ref DB URLs & data302 URLs for env install (#588)

---
 source/data-resources.rst |  4 ++--
 source/install/native.rst | 24 ++++++++++++------------
 2 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/source/data-resources.rst b/source/data-resources.rst
index 8e00f63..fcc2ef1 100644
--- a/source/data-resources.rst
+++ b/source/data-resources.rst
@@ -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/classifiers/sklearn-0.21.2/sepp-ref-dbs/sepp-refs-silva-128.qza>`_ (MD5: ``7879792a6f42c5325531de9866f5c4de``)
-- `Greengenes 13_8 SEPP reference database <https://data.qiime2.org/classifiers/sklearn-0.21.2/sepp-ref-dbs/sepp-refs-gg-13-8.qza>`_ (MD5: ``9ed215415b52c362e25cb0a8a46e1076``)
+- `Silva 128 SEPP reference database <https://data.qiime2.org/classifiers/sepp-ref-dbs/sepp-refs-silva-128.qza>`_ (MD5: ``7879792a6f42c5325531de9866f5c4de``)
+- `Greengenes 13_8 SEPP reference database <https://data.qiime2.org/classifiers/sepp-ref-dbs/sepp-refs-gg-13-8.qza>`_ (MD5: ``9ed215415b52c362e25cb0a8a46e1076``)
diff --git a/source/install/native.rst b/source/install/native.rst
index 6aefa51..2c6954d 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-2024.5 --file https://raw.githubusercontent.com/qiime2/distributions/dev/2024.5/amplicon/released/qiime2-amplicon-macos-latest-conda.yml</pre>
+            <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>
          </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-2024.5 --file https://raw.githubusercontent.com/qiime2/distributions/dev/2024.5/amplicon/released/qiime2-amplicon-macos-latest-conda.yml
+            <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
    conda activate qiime2-amplicon-2024.5
    conda config --env --set subdir osx-64</pre>
          </div>
          <div id="amplicon-linux" class="tab-pane fade">
-            <pre>conda env create -n qiime2-amplicon-2024.5 --file https://raw.githubusercontent.com/qiime2/distributions/dev/2024.5/amplicon/released/qiime2-amplicon-ubuntu-latest-conda.yml</pre>
+            <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>
          </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-2024.5 --file https://raw.githubusercontent.com/qiime2/distributions/dev/2024.5/amplicon/released/qiime2-amplicon-ubuntu-latest-conda.yml</pre>
+            <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>
          </div>
       </div>
    </div>
@@ -100,20 +100,20 @@ QIIME 2 Metagenome Distribution
             </p>
          </div>
          <div id="metagenome-macOS-intel" class="tab-pane fade">
-            <pre>conda env create -n qiime2-metagenome-2024.5 --file https://raw.githubusercontent.com/qiime2/distributions/dev/2024.5/metagenome/released/qiime2-metagenome-macos-latest-conda.yml</pre>
+            <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>
          </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-2024.5 --file https://raw.githubusercontent.com/qiime2/distributions/dev/2024.5/metagenome/released/qiime2-metagenome-macos-latest-conda.yml
+            <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
    conda activate qiime2-metagenome-2024.5
    conda config --env --set subdir osx-64</pre>
          </div>
          <div id="metagenome-linux" class="tab-pane fade">
-            <pre>conda env create -n qiime2-metagenome-2024.5 --file https://raw.githubusercontent.com/qiime2/distributions/dev/2024.5/metagenome/released/qiime2-metagenome-ubuntu-latest-conda.yml</pre>
+            <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>
          </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-2024.5 --file https://raw.githubusercontent.com/qiime2/distributions/dev/2024.5/metagenome/released/qiime2-metagenome-ubuntu-latest-conda.yml</pre>
+            <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>
          </div>
       </div>
    </div>
@@ -138,20 +138,20 @@ QIIME 2 Tiny Distribution
             </p>
          </div>
          <div id="tiny-macOS-intel" class="tab-pane fade">
-            <pre>conda env create -n qiime2-tiny-2024.5 --file https://raw.githubusercontent.com/qiime2/distributions/dev/2024.5/tiny/released/qiime2-tiny-macos-latest-conda.yml</pre>
+            <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>
          </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-2024.5 --file https://raw.githubusercontent.com/qiime2/distributions/dev/2024.5/tiny/released/qiime2-tiny-macos-latest-conda.yml
+            <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
    conda activate qiime2-tiny-2024.5
    conda config --env --set subdir osx-64</pre>
          </div>
          <div id="tiny-linux" class="tab-pane fade">
-            <pre>conda env create -n qiime2-tiny-2024.5 --file https://raw.githubusercontent.com/qiime2/distributions/dev/2024.5/tiny/released/qiime2-tiny-ubuntu-latest-conda.yml</pre>
+            <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>
          </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-2024.5 --file https://raw.githubusercontent.com/qiime2/distributions/dev/2024.5/tiny/released/qiime2-tiny-ubuntu-latest-conda.yml</pre>
+            <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>
          </div>
       </div>
    </div>