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lizgehret authored Feb 15, 2024
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2 changes: 1 addition & 1 deletion source/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,7 @@ def setup(app):

# General information about the project.
project = 'QIIME 2'
copyright = '2016-2022, QIIME 2 development team'
copyright = '2016-2024, QIIME 2 development team'
author = 'QIIME 2 development team'

# The version info for the project you're documenting, acts as replacement for
Expand Down
22 changes: 11 additions & 11 deletions source/data-resources.rst
Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,8 @@ Taxonomy classifiers for use with q2-feature-classifier

Naive Bayes classifiers trained on:

- `Silva 138 99% OTUs full-length sequences <https://data.qiime2.org/2023.9/common/silva-138-99-nb-classifier.qza>`_ (MD5: ``b8609f23e9b17bd4a1321a8971303310``)
- `Silva 138 99% OTUs from 515F/806R region of sequences <https://data.qiime2.org/2023.9/common/silva-138-99-515-806-nb-classifier.qza>`_ (MD5: ``e05afad0fe87542704be96ff483824d4``)
- `Silva 138 99% OTUs full-length sequences <https://data.qiime2.org/2024.2/common/silva-138-99-nb-classifier.qza>`_ (MD5: ``b8609f23e9b17bd4a1321a8971303310``)
- `Silva 138 99% OTUs from 515F/806R region of sequences <https://data.qiime2.org/2024.2/common/silva-138-99-515-806-nb-classifier.qza>`_ (MD5: ``e05afad0fe87542704be96ff483824d4``)
- `Greengenes2 2022.10 full length sequences <https://data.qiime2.org/classifiers/greengenes/gg_2022_10_backbone_full_length.nb.qza>`_ (MD5: ``98d34227fe67b34f62b464466cca4ffa``)
- `Greengenes2 2022.10 from 515F/806R region of sequences <https://data.qiime2.org/classifiers/greengenes/gg_2022_10_backbone.v4.nb.qza>`_ (MD5: ``43de361005ae6dcae61b078c0c835021``)

Expand Down Expand Up @@ -40,9 +40,9 @@ Weighted Taxonomic Classifiers

These 16S rRNA gene classifiers were trained with weights that take into account the fact that not all species are equally likely to be observed. If your sample comes from any of the 14 habitat types we tested, these weighted classifiers should give you superior classification precision. If your sample doesn't come from one of those habitats, they might still help. If you have the time, training with weights specific to your habitat should help even more. Weights for a range of habitats `are available here <https://github.com/BenKaehler/readytowear>`_.

- `Weighted Silva 138 99% OTUs full-length sequences <https://data.qiime2.org/2023.9/common/silva-138-99-nb-weighted-classifier.qza>`_ (MD5: ``48965bb0a9e63c411452a460d92cfc04``)
- `Weighted Greengenes 13_8 99% OTUs full-length sequences <https://data.qiime2.org/2023.9/common/gg-13-8-99-nb-weighted-classifier.qza>`_ (MD5: ``2baf87fce174c5f6c22a4c4086b1f1fe``)
- `Weighted Greengenes 13_8 99% OTUs from 515F/806R region of sequences <https://data.qiime2.org/2023.9/common/gg-13-8-99-515-806-nb-weighted-classifier.qza>`_ (MD5: ``8fb808c4af1c7526a2bdfaafa764e21f``)
- `Weighted Silva 138 99% OTUs full-length sequences <https://data.qiime2.org/2024.2/common/silva-138-99-nb-weighted-classifier.qza>`_ (MD5: ``48965bb0a9e63c411452a460d92cfc04``)
- `Weighted Greengenes 13_8 99% OTUs full-length sequences <https://data.qiime2.org/2024.2/common/gg-13-8-99-nb-weighted-classifier.qza>`_ (MD5: ``2baf87fce174c5f6c22a4c4086b1f1fe``)
- `Weighted Greengenes 13_8 99% OTUs from 515F/806R region of sequences <https://data.qiime2.org/2024.2/common/gg-13-8-99-515-806-nb-weighted-classifier.qza>`_ (MD5: ``8fb808c4af1c7526a2bdfaafa764e21f``)

Please cite the following reference, in addition to those listed above, if you use any of these weighted pre-trained classifiers:

Expand Down Expand Up @@ -77,10 +77,10 @@ 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/2023.9/common/silva-138-99-seqs.qza>`_ (MD5: ``de8886bb2c059b1e8752255d271f3010``)
- `Silva 138 SSURef NR99 full-length taxonomy <https://data.qiime2.org/2023.9/common/silva-138-99-tax.qza>`_ (MD5: ``f12d5b78bf4b1519721fe52803581c3d``)
- `Silva 138 SSURef NR99 515F/806R region sequences <https://data.qiime2.org/2023.9/common/silva-138-99-seqs-515-806.qza>`_ (MD5: ``a914837bc3f8964b156a9653e2420d22``)
- `Silva 138 SSURef NR99 515F/806R region taxonomy <https://data.qiime2.org/2023.9/common/silva-138-99-tax-515-806.qza>`_ (MD5: ``e2c40ae4c60cbf75e24312bb24652f2c``)
- `Silva 138 SSURef NR99 full-length sequences <https://data.qiime2.org/2024.2/common/silva-138-99-seqs.qza>`_ (MD5: ``de8886bb2c059b1e8752255d271f3010``)
- `Silva 138 SSURef NR99 full-length taxonomy <https://data.qiime2.org/2024.2/common/silva-138-99-tax.qza>`_ (MD5: ``f12d5b78bf4b1519721fe52803581c3d``)
- `Silva 138 SSURef NR99 515F/806R region sequences <https://data.qiime2.org/2024.2/common/silva-138-99-seqs-515-806.qza>`_ (MD5: ``a914837bc3f8964b156a9653e2420d22``)
- `Silva 138 SSURef NR99 515F/806R region taxonomy <https://data.qiime2.org/2024.2/common/silva-138-99-tax-515-806.qza>`_ (MD5: ``e2c40ae4c60cbf75e24312bb24652f2c``)


Please cite the following references if you use any of these pre-formatted files:
Expand Down Expand Up @@ -123,5 +123,5 @@ 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/2023.9/common/sepp-refs-silva-128.qza>`_ (MD5: ``7879792a6f42c5325531de9866f5c4de``)
- `Greengenes 13_8 SEPP reference database <https://data.qiime2.org/2023.9/common/sepp-refs-gg-13-8.qza>`_ (MD5: ``9ed215415b52c362e25cb0a8a46e1076``)
- `Silva 128 SEPP reference database <https://data.qiime2.org/2024.2/common/sepp-refs-silva-128.qza>`_ (MD5: ``7879792a6f42c5325531de9866f5c4de``)
- `Greengenes 13_8 SEPP reference database <https://data.qiime2.org/2024.2/common/sepp-refs-gg-13-8.qza>`_ (MD5: ``9ed215415b52c362e25cb0a8a46e1076``)
16 changes: 8 additions & 8 deletions source/install/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -38,19 +38,19 @@ option for all cases. In general we recommend the following:

.. _distributions:

QIIME 2 2023.9 distributions
QIIME 2 2024.2 distributions
----------------------------

As of 2023.9, QIIME 2 releases now include the following QIIME 2 distributions that are available for install:
As of 2024.2, QIIME 2 releases now include the following QIIME 2 distributions that are available for install:

- ``amplicon``
- ``shotgun``
- ``tiny``

QIIME 2 2023.9 Amplicon Distribution
QIIME 2 2024.2 Amplicon Distribution
....................................

The 2023.9 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins:
The 2024.2 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``
Expand All @@ -74,10 +74,10 @@ The 2023.9 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 fra
- ``q2-types``
- ``q2-vsearch``

QIIME 2 2023.9 Shotgun Distribution
QIIME 2 2024.2 Shotgun Distribution
...................................

The 2023.9 release of the QIIME 2 Shotgun Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins:
The 2024.2 release of the QIIME 2 Shotgun Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins:

- ``q2-assembly``
- ``q2-cutadapt``
Expand All @@ -98,10 +98,10 @@ The 2023.9 release of the QIIME 2 Shotgun Distribution includes the QIIME 2 fram
- ``q2-types-genomics``
- ``rescript``

QIIME 2 2023.9 Tiny Distribution
QIIME 2 2024.2 Tiny Distribution
................................

The 2023.9 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 2024.2 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``

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90 changes: 45 additions & 45 deletions source/install/native.rst
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Expand Up @@ -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 2023.9 distribution of your choice within the environment.
the QIIME 2 2024.2 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>-2023.9``
to indicate what QIIME 2 release is installed (i.e. ``2023.9``).
In this example, we'll name the environments ``qiime2-<distro>-2024.2``
to indicate what QIIME 2 release is installed (i.e. ``2024.2``).

QIIME 2 Amplicon Distribution
.............................
Expand All @@ -70,32 +70,32 @@ 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-2023.9-py38-osx-conda.yml
conda env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-osx-conda.yml</pre>
<pre>wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-osx-conda.yml
conda env create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-osx-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-amplicon-2023.9-py38-osx-conda.yml</pre>
<pre>rm qiime2-amplicon-2024.2-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 conda env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-osx-conda.yml
conda activate qiime2-amplicon-2023.9
<pre>wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-osx-conda.yml
conda activate qiime2-amplicon-2024.2
conda config --env --set subdir osx-64</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-amplicon-2023.9-py38-osx-conda.yml</pre>
<pre>rm qiime2-amplicon-2024.2-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
conda env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-linux-conda.yml</pre>
<pre>wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-linux-conda.yml
conda env create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-linux-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-amplicon-2023.9-py38-linux-conda.yml</pre>
<pre>rm qiime2-amplicon-2024.2-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
conda env create -n qiime2-amplicon-2023.9 --file qiime2-amplicon-2023.9-py38-linux-conda.yml</pre>
<pre>wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-linux-conda.yml
conda env create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-linux-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-amplicon-2023.9-py38-linux-conda.yml</pre>
<pre>rm qiime2-amplicon-2024.2-py38-linux-conda.yml</pre>
</div>
</div>
</div>
Expand All @@ -120,32 +120,32 @@ QIIME 2 Shotgun Distribution
</p>
</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
conda env create -n qiime2-shotgun-2023.9 --file qiime2-shotgun-2023.9-py38-osx-conda.yml</pre>
<pre>wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.2-py38-osx-conda.yml
conda env create -n qiime2-shotgun-2024.2 --file qiime2-shotgun-2024.2-py38-osx-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-shotgun-2023.9-py38-osx-conda.yml</pre>
<pre>rm qiime2-shotgun-2024.2-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 conda env create -n qiime2-shotgun-2023.9 --file qiime2-shotgun-2023.9-py38-osx-conda.yml
conda activate qiime2-shotgun-2023.9
<pre>wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.2-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n qiime2-shotgun-2024.2 --file qiime2-shotgun-2024.2-py38-osx-conda.yml
conda activate qiime2-shotgun-2024.2
conda config --env --set subdir osx-64</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-shotgun-2023.9-py38-osx-conda.yml</pre>
<pre>rm qiime2-shotgun-2024.2-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
conda env create -n qiime2-shotgun-2023.9 --file qiime2-shotgun-2023.9-py38-linux-conda.yml</pre>
<pre>wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.2-py38-linux-conda.yml
conda env create -n qiime2-shotgun-2024.2 --file qiime2-shotgun-2024.2-py38-linux-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-shotgun-2023.9-py38-linux-conda.yml</pre>
<pre>rm qiime2-shotgun-2024.2-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
conda env create -n qiime2-shotgun-2023.9 --file qiime2-shotgun-2023.9-py38-linux-conda.yml</pre>
<pre>wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.2-py38-linux-conda.yml
conda env create -n qiime2-shotgun-2024.2 --file qiime2-shotgun-2024.2-py38-linux-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-shotgun-2023.9-py38-linux-conda.yml</pre>
<pre>rm qiime2-shotgun-2024.2-py38-linux-conda.yml</pre>
</div>
</div>
</div>
Expand All @@ -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-2023.9-py38-osx-conda.yml
conda env create -n qiime2-tiny-2023.9 --file qiime2-tiny-2023.9-py38-osx-conda.yml</pre>
<pre>wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.2-py38-osx-conda.yml
conda env create -n qiime2-tiny-2024.2 --file qiime2-tiny-2024.2-py38-osx-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-tiny-2023.9-py38-osx-conda.yml</pre>
<pre>rm qiime2-tiny-2024.2-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 conda env create -n qiime2-tiny-2023.9 --file qiime2-tiny-2023.9-py38-osx-conda.yml
conda activate qiime2-tiny-2023.9
<pre>wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.2-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n qiime2-tiny-2024.2 --file qiime2-tiny-2024.2-py38-osx-conda.yml
conda activate qiime2-tiny-2024.2
conda config --env --set subdir osx-64</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-tiny-2023.9-py38-osx-conda.yml</pre>
<pre>rm qiime2-tiny-2024.2-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
conda env create -n qiime2-tiny-2023.9 --file qiime2-tiny-2023.9-py38-linux-conda.yml</pre>
<pre>wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.2-py38-linux-conda.yml
conda env create -n qiime2-tiny-2024.2 --file qiime2-tiny-2024.2-py38-linux-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-tiny-2023.9-py38-linux-conda.yml</pre>
<pre>rm qiime2-tiny-2024.2-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
conda env create -n qiime2-tiny-2023.9 --file qiime2-tiny-2023.9-py38-linux-conda.yml</pre>
<pre>wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.2-py38-linux-conda.yml
conda env create -n qiime2-tiny-2024.2 --file qiime2-tiny-2024.2-py38-linux-conda.yml</pre>
<span>OPTIONAL CLEANUP</span>
<pre>rm qiime2-tiny-2023.9-py38-linux-conda.yml</pre>
<pre>rm qiime2-tiny-2024.2-py38-linux-conda.yml</pre>
</div>
</div>
</div>
Expand All @@ -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>-2023.9
conda activate qiime2-<distro>-2024.2

To deactivate an environment, run ``conda deactivate``.

Expand Down Expand Up @@ -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 2023.9 can be activated (or reactivated) by running
or deactivated, QIIME 2 2024.2 can be activated (or reactivated) by running
the following command:

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

conda activate qiime2-<distro>-2023.9
conda activate qiime2-<distro>-2024.2

To determine the currently active conda environment, run the following
command and look for the line that starts with "active environment":
Expand Down
4 changes: 2 additions & 2 deletions source/install/virtual/docker.rst
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ In a terminal with Docker activated, run:
.. command-block::
:no-exec:

docker pull quay.io/qiime2/amplicon:2023.9
docker pull quay.io/qiime2/amplicon:2024.2

3. Confirm the installation
---------------------------
Expand All @@ -24,4 +24,4 @@ Run the following to confirm that the image was successfully fetched.
.. command-block::
:no-exec:

docker run -t -i -v $(pwd):/data quay.io/qiime2/amplicon:2023.9 qiime
docker run -t -i -v $(pwd):/data quay.io/qiime2/amplicon:2024.2 qiime
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