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How to install other versions of RESCRIPt.

Minimal RESCRIPt environment (2023.9 and later)

To make use of the latest "minimal" RESCRIPt release, some components of QIIME 2 (releases 2023.9 and later) are required:

First create a conda environment and install relevant dependencies using either conda or mamba.

Note: update {ENV_VERSION} in the commands below to match the QIIME 2 release.

conda create -y -n rescript
conda activate rescript

conda install \
  -c https://packages.qiime2.org/qiime2/{ENV_VERSION}/shotgun/passed/ \
  -c https://packages.qiime2.org/qiime2/{ENV_VERSION}/amplicon/passed/ \
  -c conda-forge -c bioconda -c qiime2 -c defaults \
  qiime2 q2cli q2templates q2-types q2-types-genomics q2-longitudinal q2-feature-classifier \
  "pandas>=0.25.3" xmltodict ncbi-datasets-pylib rescript

qiime rescript --help

Install within the QIIME 2 2023.9 release:

For this version of QIIME 2, RESCRIPt is included within the qiime2-shotgun-2023.9 distribution. You'll be able to run your RESCRIPt commands within this environment, then switch back to qiime2-amplicon-2023.9 environment if needed. It is possible to install RESCRIPt within qiime2-amplicon-2023.9. You can try via the following commands:

conda activate qiime2-amplicon-2023.9

conda install -c conda-forge -c bioconda -c qiime2 \
    -c https://packages.qiime2.org/qiime2/2023.9/shotgun/passed/  \
    -c defaults   xmltodict 'q2-types-genomics>2023.5' ncbi-datasets-pylib rescript

qiime rescript --help

Install within the QIIME 2 releases 2023.2 - 2023.7.

Current releases of RESCRIPt should generally be compatable with these QIIME 2 versions. If not, please download the corresponding RESCRIPt release and consult that version's README file for appropriate Installation instructions.

Note: update {ENV_VERSION} in the commands below to match the QIIME 2 release.

conda activate qiime2-{ENV_VERSION}

conda install -c conda-forge -c bioconda -c qiime2 \
    -c https://packages.qiime2.org/qiime2/{ENV_VERSION}/passed/ \
    -c defaults xmltodict 'q2-types-genomics>2023.2' ncbi-datasets-pylib

Install source:

pip install git+https://github.com/bokulich-lab/RESCRIPt.git

qiime rescript --help

Install within prior releases of QIIME 2 2022.8 and earlier.

Download any of the prior Releases and consult that version's README file for appropriate Installation instructions.