diff --git a/README.md b/README.md index b80a4a7..df784e8 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@


## Installation -You can install q2-fondue using mamba in a conda environment of its own (option 1) or in an existing QIIME 2 environment (option 2) by following the steps described below. The current q2-fondue version supports QIIME 2 **v2021.4** or higher. Alternatively, a minimal Docker image is available to run q2-fondue methods (option 3 below). +You can install q2-fondue using mamba in a conda environment of its own (option 1) or in an existing QIIME 2 environment (option 2) by following the steps described below. The current q2-fondue version supports QIIME 2 **v2021.4** or higher. To install q2-fondue with a version <= 2023.7 see section ["Installing q2-fondue with version <= 2023.7"](#legacy).Alternatively, a minimal Docker image is available to run q2-fondue methods (option 3 below). For both options 1 and 2 make sure to start by installing [mamba](https://mamba.readthedocs.io/en/latest/index.html) in your base environment: ```shell @@ -23,7 +23,7 @@ conda install mamba -n base -c conda-forge * Create and activate a conda environment with the required dependencies: ```shell mamba create -y -n fondue \ - -c https://packages.qiime2.org/qiime2/2023.7/tested/ \ + -c https://packages.qiime2.org/qiime2/2024.5/metagenome/released/ \ -c conda-forge -c bioconda -c defaults \ q2cli q2-fondue @@ -33,11 +33,11 @@ Now, don't forget to run [the mandatory configuration step](#mandatory-configura ### Option 2: Install fondue within existing QIIME 2 environment * Install QIIME 2 within a conda environment as described in [the official user documentation](https://docs.qiime2.org/). -* Activate the QIIME 2 environment (v2022.8 or higher) and install fondue within while making sure that the used conda channel matches the version of the QIIME 2 environment (replace below `{ENV_VERSION}` with the version number of your QIIME 2 environment): +* Activate the QIIME 2 environment (v2024.5 or higher) and install fondue within while making sure that the used conda channel matches the version of the QIIME 2 environment (replace below `{ENV_VERSION}` with the version number of your QIIME 2 environment): ``` conda activate qiime2-{ENV_VERSION} mamba install -y \ - -c https://packages.qiime2.org/qiime2/{ENV_VERSION}/tested/ \ + -c https://packages.qiime2.org/qiime2/{ENV_VERSION}/metagenome/released/ \ -c conda-forge -c bioconda -c defaults \ q2-fondue ``` @@ -63,6 +63,9 @@ vdb-config -i vdb-config --proxy --proxy-disable no ``` +### [Installing q2-fondue with version <= 2023.7](#legacy) +To install fondue with a version <= 2023.7 in either a minimal environment (option 1) or within an existing QIIME2 environment (option 2), you have to edit the channel to: `https://packages.qiime2.org/qiime2/{ENV_VERSION}/tested/` (inserting the respective version number `{ENV_VERSION}`). + ### Option 3: Use fondue via a public Docker image Use containerization to integrate q2-fondue into your pipelines, or simply run reproducibly without the need for heavyweight package managers. [Read more about Docker here.](https://www.docker.com/get-started/)