From efb853e8b82c9956d0cc54ee44375abcc1e03fec Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Thu, 24 Apr 2025 10:48:39 -0700 Subject: [PATCH] Revert "MAINT: update listed plugins for each distro in 2025.4 (#594)" This reverts commit 0ef07c0eb5b648a2208eea073945415018922480. --- source/install/index.rst | 41 +++++++++++++++++----------------------- 1 file changed, 17 insertions(+), 24 deletions(-) diff --git a/source/install/index.rst b/source/install/index.rst index d4b8a77..044aae4 100644 --- a/source/install/index.rst +++ b/source/install/index.rst @@ -38,20 +38,20 @@ option for all cases. In general we recommend the following: .. _distributions: -QIIME 2 2025.4 distributions ----------------------------- +QIIME 2 2024.10 distributions +----------------------------- -As of 2025.4, QIIME 2 releases now include the following QIIME 2 distributions that are available for install: +As of 2024.10, QIIME 2 releases now include the following QIIME 2 distributions that are available for install: - ``amplicon`` -- ``moshpit`` +- ``metagenome`` - ``pathogenome`` - ``tiny`` -QIIME 2 2025.4 Amplicon Distribution -.................................... +QIIME 2 2024.10 Amplicon Distribution +..................................... -The 2025.4 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins: +The 2024.10 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`` @@ -71,19 +71,16 @@ The 2025.4 release of the QIIME 2 Amplicon Distribution includes the QIIME 2 fra - ``q2-quality-control`` - ``q2-quality-filter`` - ``q2-sample-classifier`` -- ``q2-stats`` - ``q2-taxa`` - ``q2-types`` -- ``q2-vizard`` - ``q2-vsearch`` - ``rescript`` -QIIME 2 2025.4 MOSHPIT (formerly Metagenome) Distribution -......................................................... +QIIME 2 2024.10 Metagenome Distribution +....................................... -The 2025.4 release of the QIIME 2 MOSHPIT (formerly Metagenome) Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins: +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-alignment`` - ``q2-assembly`` - ``q2-composition`` - ``q2-cutadapt`` @@ -101,17 +98,15 @@ The 2025.4 release of the QIIME 2 MOSHPIT (formerly Metagenome) Distribution inc - ``q2-quality-filter`` - ``q2-sample-classifier`` - ``q2-sapienns`` -- ``q2-sourmash`` - ``q2-taxa`` - ``q2-types`` -- ``q2-vizard`` - ``q2-vsearch`` - ``rescript`` -QIIME 2 2025.4 Pathogenome Distribution -....................................... +QIIME 2 2024.10 Pathogenome Distribution +........................................ -The 2025.4 release of the QIIME 2 Pathogenome Distribution includes the QIIME 2 framework, ``q2cli`` (a QIIME 2 command-line interface) and the following plugins: +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`` @@ -119,7 +114,6 @@ The 2025.4 release of the QIIME 2 Pathogenome Distribution includes the QIIME 2 - ``q2-feature-classifier`` - ``q2-feature-table`` - ``q2-longitudinal`` -- ``q2-metadata`` - ``q2-quality-control`` - ``q2-sample-classifier`` - ``q2-taxa`` @@ -128,15 +122,14 @@ The 2025.4 release of the QIIME 2 Pathogenome Distribution includes the QIIME 2 - ``q2-vizard`` - ``rescript`` -QIIME 2 2025.4 Tiny Distribution -................................ +QIIME 2 2024.10 Tiny Distribution +................................. -The 2025.4 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 2024.10 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-metadata`` - ``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, MOSHPIT or Pathogenome 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.