Skip to content

Commit

Permalink
MAINT: remove mamba from install docs (#568)
Browse files Browse the repository at this point in the history
  • Loading branch information
@lizgehret
lizgehret authored Nov 16, 2023
1 parent 6f2aba2 commit cf5aad6
Showing 1 changed file with 12 additions and 20 deletions.
32 changes: 12 additions & 20 deletions source/install/native.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -38,14 +38,6 @@ Installing ``wget``

conda install wget

Installing ``mamba``
....................

.. command-block::
:no-exec:

conda install mamba

Install QIIME 2 within a ``conda`` environment
----------------------------------------------

Expand Down Expand Up @@ -79,29 +71,29 @@ QIIME 2 Amplicon Distribution
</div>
<div id="amplicon-macOS-intel" class="tab-pane fade">
<pre>wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2023.9-py38-osx-conda.yml
mamba env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-osx-conda.yml</pre>
conda env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-osx-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-amplicon-2023.9-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-2023.9-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 mamba env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-osx-conda.yml
conda activate qiime2-amplicon-2023.9
conda config --env --set subdir osx-64</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-amplicon-2023.9-py38-osx-conda.yml</pre>
</div>
<div id="amplicon-linux" class="tab-pane fade">
<pre>wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2023.9-py38-linux-conda.yml
mamba env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-linux-conda.yml</pre>
conda env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-linux-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-amplicon-2023.9-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-2023.9-py38-linux-conda.yml
mamba env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-linux-conda.yml</pre>
conda env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-linux-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-amplicon-2023.9-py38-linux-conda.yml</pre>
</div>
Expand Down Expand Up @@ -129,29 +121,29 @@ QIIME 2 Shotgun Distribution
</div>
<div id="shotgun-macOS-intel" class="tab-pane fade">
<pre>wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2023.9-py38-osx-conda.yml
mamba env create -n qiime2-shotgun-2023.9 --file qiime2-shotgun-2023.9-py38-osx-conda.yml</pre>
conda env create -n qiime2-shotgun-2023.9 --file qiime2-shotgun-2023.9-py38-osx-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-shotgun-2023.9-py38-osx-conda.yml</pre>
</div>
<div id="shotgun-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-2023.9-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 mamba env create -n qiime2-shotgun-2023.9 --file qiime2-shotgun-2023.9-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n qiime2-shotgun-2023.9 --file qiime2-shotgun-2023.9-py38-osx-conda.yml
conda activate qiime2-shotgun-2023.9
conda config --env --set subdir osx-64</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-shotgun-2023.9-py38-osx-conda.yml</pre>
</div>
<div id="shotgun-linux" class="tab-pane fade">
<pre>wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2023.9-py38-linux-conda.yml
mamba env create -n qiime2-shotgun-2023.9 --file qiime2-shotgun-2023.9-py38-linux-conda.yml</pre>
conda env create -n qiime2-shotgun-2023.9 --file qiime2-shotgun-2023.9-py38-linux-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-shotgun-2023.9-py38-linux-conda.yml</pre>
</div>
<div id="shotgun-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-2023.9-py38-linux-conda.yml
mamba env create -n qiime2-shotgun-2023.9 --file qiime2-shotgun-2023.9-py38-linux-conda.yml</pre>
conda env create -n qiime2-shotgun-2023.9 --file qiime2-shotgun-2023.9-py38-linux-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-shotgun-2023.9-py38-linux-conda.yml</pre>
</div>
Expand Down Expand Up @@ -179,29 +171,29 @@ QIIME 2 Tiny Distribution
</div>
<div id="tiny-macOS-intel" class="tab-pane fade">
<pre>wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2023.9-py38-osx-conda.yml
mamba env create -n qiime2-tiny-2023.9 --file qiime2-tiny-2023.9-py38-osx-conda.yml</pre>
conda env create -n qiime2-tiny-2023.9 --file qiime2-tiny-2023.9-py38-osx-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-tiny-2023.9-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-2023.9-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 mamba env create -n qiime2-tiny-2023.9 --file qiime2-tiny-2023.9-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n qiime2-tiny-2023.9 --file qiime2-tiny-2023.9-py38-osx-conda.yml
conda activate qiime2-tiny-2023.9
conda config --env --set subdir osx-64</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-tiny-2023.9-py38-osx-conda.yml</pre>
</div>
<div id="tiny-linux" class="tab-pane fade">
<pre>wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2023.9-py38-linux-conda.yml
mamba env create -n qiime2-tiny-2023.9 --file qiime2-tiny-2023.9-py38-linux-conda.yml</pre>
conda env create -n qiime2-tiny-2023.9 --file qiime2-tiny-2023.9-py38-linux-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-tiny-2023.9-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-2023.9-py38-linux-conda.yml
mamba env create -n qiime2-tiny-2023.9 --file qiime2-tiny-2023.9-py38-linux-conda.yml</pre>
conda env create -n qiime2-tiny-2023.9 --file qiime2-tiny-2023.9-py38-linux-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-tiny-2023.9-py38-linux-conda.yml</pre>
</div>
Expand Down

0 comments on commit cf5aad6

Please sign in to comment.