From e31a6a8a185b5d795fc4ce342cc76ad418c43e9f Mon Sep 17 00:00:00 2001 From: Adam Rivers Date: Mon, 15 Apr 2024 11:59:35 -0400 Subject: [PATCH 1/2] simplified install instructions --- README.rst | 60 +++++++++++++++++++++++++++++++++++------------------- 1 file changed, 39 insertions(+), 21 deletions(-) diff --git a/README.rst b/README.rst index 283f63f..3296daf 100644 --- a/README.rst +++ b/README.rst @@ -61,41 +61,57 @@ QIIME2 is being used. .. _`QIIME2 Plugin`: https://github.com/USDA-ARS-GBRU/q2_itsxpress -Environment with or without QIIME2 ------------------------------------ -Create a new conda environment before installing ITSxpress. +Installing ITSxpress for use as a QIIME2 Plugin +---------------------------------------------------- -If using QIIME2, follow the installation instructions on their wiki: https://docs.qiime2.org/2022.11/install/native/ +To install ITSxpress as a plugin for QIIME 2 first install QIIME 2 as a separate Conda/Mamba environemnt using thier instructions +https://docs.qiime2.org/2024.2/install/ then add ITSxress to the QIIME 2 Conda environment. The examples below are for QIIME2 2 +version 2024.2 an so please update the commands if you want a newer release. + -As of now ITSxpress is compatible with newest versions of QIIME2. The following instructions are for QIIME2 2022.11. +For Linux: -Example for OSX installation, please see Qiime documentation for other operating systems: +.. code-block:: bash + wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-linux-conda.yml + mamba create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-linux-conda.yml + mamba activate qiime2-amplicon-2024.2 + mamba install ITSxpress + qiime dev refresh-cache + +For maxOS (Intel) and OS X: .. code-block:: bash - wget https://data.qiime2.org/distro/core/qiime2-2022.11-py38-osx-conda.yml - mamba env create -n qiime2-2022.11 --file qiime2-2022.11-py38-osx-conda.yml - mamba activate qiime2-2022.11 + wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-osx-conda.yml + mamba create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-osx-conda.yml + mamba activate qiime2-amplicon-2024.2 + mamba install ITSxpress + qiime dev refresh-cache -If you are only installing the command line version of ITSxpress and not QIIME2: +For macOS (Arm / Apple Silicon): .. code-block:: bash - mamba env create -n ITSxpress - mamba activate ITSxpress + wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-osx-conda.yml + CONDA_SUBDIR=osx-64 mamba create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-osx-conda.yml + mamba activate qiime2-amplicon-2024.2 + mamba config --env --set subdir osx-64 + mamba install ITSxpress + qiime dev refresh-cache -Installation -------------- -Within either conda environment, described above, ITSxpress can be installed from: -1. Bioconda: (preferred method because it handles dependencies, **Pip is no longer maintained for ITSxpress>=2.0.0**): +Installing ITSxpress for standalone use +------------------------------------------- + +For Linux, maxOS (Intel), and OS X: .. code-block:: bash - mamba install -c bioconda itsxpress + mamba create -n itsxpressenv -c bioconda -c conda-forge itsxpress + mamba activate itsxpressenv -1.1 Bioconda installation for Apple Silicon (M1, M2, M3, etc.) installation example: +For macOS (Arm/Apple Silicon): .. code-block:: bash @@ -103,11 +119,13 @@ Within either conda environment, described above, ITSxpress can be installed fro mamba activate itsxpressenv conda config --env --set subdir osx-64 -2. The Github repository: https://github.com/USDA-ARS-GBRU/itsxpress -.. code-block:: bash +Running ITSxpress as a Docker container +------------------------------------------- - git clone https://github.com/USDA-ARS-GBRU/itsxpress.git +.. code-block:: bash + docker pull ghcr.io/usda-ars-gbru/itsxpress + docker run [Options...] itsxpress Dependencies From 5d300e5ef58993d39f7b483dfc1b136cf8d0efea Mon Sep 17 00:00:00 2001 From: Adam Rivers Date: Mon, 15 Apr 2024 12:00:57 -0400 Subject: [PATCH 2/2] simplified install instructions --- README.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.rst b/README.rst index 3296daf..0051dbb 100644 --- a/README.rst +++ b/README.rst @@ -72,6 +72,7 @@ version 2024.2 an so please update the commands if you want a newer release. For Linux: .. code-block:: bash + wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-linux-conda.yml mamba create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-linux-conda.yml mamba activate qiime2-amplicon-2024.2 @@ -124,6 +125,7 @@ Running ITSxpress as a Docker container ------------------------------------------- .. code-block:: bash + docker pull ghcr.io/usda-ars-gbru/itsxpress docker run [Options...] itsxpress