updated README install instructions

README.md

@@ -13,37 +13,28 @@ RESCRIPt is a python 3 package to support a variety of operations for managing a
 
 RESCRIPt will be installable as conda package in the near future. In the meantime, we provide two routes for source installation: a minimal RESCRIPt environment, or within an existing QIIME 2 environment:
 
-### Option 1: Minimal RESCRIPt environment:
-First create a conda environment and install relevant dependencies:
+### Option 1: Installed as part of a QIIME 2 distribution.
 
-```
-conda create -y -n rescript
-conda activate rescript
-conda install \
-  -c conda-forge -c bioconda -c qiime2 \
-  -c https://packages.qiime2.org/qiime2/2024.2/amplicon/passed/ \
-  -c defaults qiime2 q2cli q2templates q2-types q2-longitudinal q2-feature-classifier \
-  'q2-types-genomics>2023.2' "pandas>=0.25.3" xmltodict ncbi-datasets-pylib
-```
-Install source:
+For QIIME 2 versions `2023.9` and later, RESCRIPt is installed as part of the QIIME 2 "Shotgun Distribution", as outlined in the [QIIME 2 Documentation](https://docs.qiime2.org/). RESCRIPt is available as part of the "Amplicon Distrubtion" for QIIME 2 releases `2024.2` and later.
 
-```
-pip install git+https://github.com/bokulich-lab/RESCRIPt.git
+### Option 2: Minimal RESCRIPt environment 
 
-qiime rescript --help
-```
+To make use of the latest "minimal" RESCRIPt release, some components of QIIME 2 (releases `2023.9` and later) are required:
 
-### Option 2: Install within QIIME 2 environments `2024.2` and later.
-This approach assumes you have the latest version of QIIME 2 installed. If not, please refer to the [QIIME 2 installation instructions](https://docs.qiime2.org/2024.2/install/native/). *Make sure the qiime version within the 
-http string matches the version of the active qiime environment.*
+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 activate qiime2-amplicon-2024.2
-
-conda install -c conda-forge -c bioconda -c qiime2 \
-    -c https://packages.qiime2.org/qiime2/2024.2/amplicon/passed/ \
-    -c defaults xmltodict 'q2-types-genomics>2023.2' ncbi-datasets-pylib
+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
 ```
+
 Install source:
 
 ```
@@ -52,10 +43,12 @@ pip install git+https://github.com/bokulich-lab/RESCRIPt.git
 qiime rescript --help
 ```
 
-### Prior versions of RESCRIPt.
-For details on how to install prior versions of RESCRIPt, please see the `install-prior-versions.md` document.
+### Prior versions of RESCRIPt / QIIME 2.
+
+For details on how to install prior versions of RESCRIPt / QIIME 2, please see the `install-prior-versions.md` document.
 
 ### Read help documentation
+
 To view a help menu for using rescript via the QIIME 2 CLI:
 ```
 qiime dev refresh-cache
@@ -77,6 +70,7 @@ These tutorials demonstrate some of the basic functionality of RESCRIPt, via the
 Examples of visualizations produced by RESCRIPt actions can be found in this [Visualization Gallery](https://forum.qiime2.org/t/processing-filtering-and-evaluating-the-silva-database-and-other-reference-sequence-data-with-rescript/15494#heading--seventeenth-header). Other code examples can be found [here](https://github.com/bokulich-lab/db-benchmarks-2020).
 
 ## Getting Help
+
 Problem? Suggestion? Technical errors and user support requests can be filed on the [QIIME 2 Forum](https://forum.qiime2.org/).