docs(installation): Update Bioconda install documentation and README.md.

README.md

@@ -7,16 +7,37 @@
 [![Docker Image Version (latest by date)](https://img.shields.io/docker/v/ecogenomic/gtdbtk?sort=date&color=299bec&label=docker)](https://hub.docker.com/r/ecogenomic/gtdbtk)
 [![Docker Pulls](https://img.shields.io/docker/pulls/ecogenomic/gtdbtk?color=299bec&label=pulls)](https://hub.docker.com/r/ecogenomic/gtdbtk)
 
-<b>[GTDB-Tk v2.1.0](https://ecogenomics.github.io/GTDBTk/announcements.html) was released on May 11, 2022. Upgrading is recommended.</b>  
-<b> Please note v2.1.0+ is not compatible with GTDB-Tk package [R207_v1](https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_data.tar.gz). It is necessary to upgrade to GTDB-Tk package [R207_v2](https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_v2_data.tar.gz).</b>
+<b>GTDB-Tk v2.1.0+ requires an updated reference package ([R207_v2](https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_v2_data.tar.gz)), [read more](https://ecogenomics.github.io/GTDBTk/installing/index.html#gtdb-tk-reference-data).</b>
 
-GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy ([GTDB](https://gtdb.ecogenomic.org/)). It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the [GNU General Public License (Version 3)](https://www.gnu.org/licenses/gpl-3.0.en.html).
+GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based 
+on the Genome Database Taxonomy ([GTDB](https://gtdb.ecogenomic.org/)). It is designed to work with recent advances that 
+allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. 
+It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the 
+[GNU General Public License (Version 3)](https://www.gnu.org/licenses/gpl-3.0.en.html).
 
-Notifications about GTDB-Tk releases will be available through the [GTDB Twitter](https://twitter.com/ace_gtdb) account and the [GTDB Announcements Forum](https://forum.gtdb.ecogenomic.org/c/announcements/10).
+Notifications about GTDB-Tk releases will be available through the [GTDB Twitter](https://twitter.com/ace_gtdb) 
+account and the [GTDB Announcements Forum](https://forum.gtdb.ecogenomic.org/c/announcements/10).
 
-Please post questions and issues related to GTDB-Tk on the Issues section of the GitHub repository. Questions related to the [GTDB](https://gtdb.ecogenomic.org/) can be posted on the [GTDB Forum](https://forum.gtdb.ecogenomic.org/) or sent to the [GTDB team](https://gtdb.ecogenomic.org/about).
+Please post questions and issues related to GTDB-Tk on the Issues section of the GitHub repository. Questions 
+related to the [GTDB](https://gtdb.ecogenomic.org/) can be posted on the [GTDB Forum](https://forum.gtdb.ecogenomic.org/) 
+or sent to the [GTDB team](https://gtdb.ecogenomic.org/about).
 
-## New Features
+
+## 🚀 Getting started
+
+Be sure to check the [hardware requirements](https://ecogenomics.github.io/GTDBTk/installing/index.html), then choose your preferred method:
+
+* [Bioconda](https://ecogenomics.github.io/GTDBTk/installing/bioconda.html)
+* [Docker](https://ecogenomics.github.io/GTDBTk/installing/docker.html)
+* [pip](https://ecogenomics.github.io/GTDBTk/installing/pip.html)
+
+
+## 📖 Documentation
+
+Documentation for GTDB-Tk can be found [here](https://ecogenomics.github.io/GTDBTk/).
+
+
+## ✨ New Features
 
 GTDB-Tk v2.1.0 includes the following new features:
 - GTDB-TK now uses a **divide-and-conquer** approach where the bacterial reference tree is split into multiple **class**-level subtrees. This reduces the memory requirements of GTDB-Tk from **320 GB** of RAM when using the full GTDB R07-RS207 reference tree to approximately **55 GB**. A manuscript describing this approach is in preparation. If you wish to continue using the full GTDB reference tree use the `--full-tree` flag.  
@@ -26,10 +47,7 @@ This is the main change from v2.0.0. The split tree approach has been modified f
 - `--write_single_copy_genes` flag in now available in the `classify_wf` and `de_novo_wf` workflows.
 
 
-## Documentation
-Documentation for GTDB-Tk can be found [here](https://ecogenomics.github.io/GTDBTk/).
-
-## References
+## 📚 References
 
 GTDB-Tk is described in:
 
@@ -53,6 +71,7 @@ We strongly encourage you to cite the following 3rd party dependencies:
 * Eddy SR. 2011. [Accelerated profile HMM searches](https://www.ncbi.nlm.nih.gov/pubmed/22039361). <i>PLOS Comp. Biol.</i>, 7:e1002195.
 * Ondov BD, et al. 2016. [Mash: fast genome and metagenome distance estimation using MinHash](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x). <i>Genome Biol</i> 17, 132. doi: 10.1186/s13059-016-0997-x.
 
-## Copyright
+
+## © Copyright
 
 Copyright 2017 Pierre-Alain Chaumeil. See LICENSE for further details.

docs/src/installing/bioconda.rst

@@ -3,28 +3,32 @@
 Bioconda
 ========
 
-Step 1: Install anaconda (if not already done)
-----------------------------------------------
+Step 1: Install conda (if not already done)
+-------------------------------------------
 
-Ensure that ``conda`` on the system path. It is recommended to download `miniconda <https://docs.conda.io/en/latest/miniconda.html>`_.
+We strongly recommend using `Mamba <https://mamba.readthedocs.io/en/latest/installation.html>`_ (much faster!) over `miniconda <https://docs.conda.io/en/latest/miniconda.html>`_/`conda <https://docs.conda.io/projects/conda/en/stable/user-guide/install/index.html>`_, but all will work.
 
 
 Step 2: Create the GTDB-Tk environment
 --------------------------------------
 
-.. note:: It is strongly recommended to create a new GTDB-Tk environment for each version of GTDB-Tk released.
+It is strongly recommended to create a new conda environment for each version of GTDB-Tk released.
 
-GTDB-Tk package requires third-party packages from the ``conda-forge`` and ``bioconda`` channels.
+.. warning:: You must always specify the version of GTDB-Tk, as conda may try to install a **very old version (v1.0.2)**.
 
 
+GTDB-Tk requires third-party packages from the ``conda-forge`` and ``bioconda`` channels, make sure to
+specify those channels in that order!
+
 .. code-block:: bash
 
-    # latest version
-    conda create -n gtdbtk -c conda-forge -c bioconda gtdbtk
+    # NOTE: replace 2.1.1 with the version you wish to install
 
-    # specific version (replace 1.3.0 with the version you wish to install, recommended)
-    conda create -n gtdbtk-1.3.0 -c conda-forge -c bioconda gtdbtk=1.3.0
+    # using conda
+    conda create -n gtdbtk-2.1.1 -c conda-forge -c bioconda gtdbtk=2.1.1
 
+    # using mamba (alternative)
+    mamba create -n gtdbtk-2.1.1 -c conda-forge -c bioconda gtdbtk=2.1.1
 
 Step 3: Download and alias the GTDB-Tk reference data
 -----------------------------------------------------
@@ -35,7 +39,7 @@ containing the unarchived :ref:`installing#gtdbtk-reference-data`.
 Automatically
 ^^^^^^^^^^^^^
 
-The conda package is bundled with a script ``download-db.sh`` `(located here) <https://github.com/bioconda/bioconda-recipes/blob/master/recipes/gtdbtk/download-db.sh>`_
+The conda package is bundled with a script ``download-db.sh`` `(source) <https://github.com/bioconda/bioconda-recipes/blob/master/recipes/gtdbtk/download-db.sh>`_
 that will automatically download, and extract the GTDB-Tk reference data. The script will be on the system path so simply run:
 
 .. code-block:: bash
@@ -47,14 +51,13 @@ that will automatically download, and extract the GTDB-Tk reference data. The sc
 Manually
 ^^^^^^^^
 
-You can automatically alias ``GTDBTK_DATA_PATH`` whenever the environment is activated by editing ``{gtdbtk environment path}/etc/conda/activate.d/gtdbtk.sh``, e.g.:
+You can automatically alias ``GTDBTK_DATA_PATH`` whenever the environment is activated by
+`setting environment-specific variables <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#setting-environment-variables>`_, e.g.:
 
 .. code-block:: bash
 
-    # Determine the GTDB-Tk environment path
-    conda activate gtdbtk-1.3.0
-    which gtdbtk
-    # /miniconda3/envs/gtdbtk-1.3.0/bin/gtdbtk
+    # Activate the GTDB-Tk conda environment
+    conda activate gtdbtk-2.1.1
 
-    # Edit the activate file
-    echo "export GTDBTK_DATA_PATH=/path/to/release/package/" > /miniconda3/envs/gtdbtk-1.3.0/etc/conda/activate.d/gtdbtk.sh
+    # Set the environment variable to the directory containing the GTDB-Tk reference data
+    conda env config vars set GTDBTK_DATA_PATH="/path/to/unarchived/gtdbtk/data";

docs/src/installing/index.rst

@@ -3,9 +3,8 @@
 Installing GTDB-Tk
 ==================
 
-GTDB-Tk is available through multiple sources.
-
-If you are unsure which source to install, Bioconda is generally the easiest.
+GTDB-Tk is available through multiple sources, you only need to choose one.
+If you are unsure which one to choose, Bioconda is generally the easiest.
 
 
 Sources
@@ -15,11 +14,11 @@ Sources
 .. toctree::
    :maxdepth: 1
 
-   pip
    bioconda
+   pip
    docker
 
-Alternatively, GTDB-Tk can be run online through `KBase <https://kbase.us/applist/apps/kb_gtdbtk/run_kb_gtdbtk>`_ (third party).
+Alternatively, GTDB-Tk can be run online through `KBase <https://kbase.us/applist/apps/kb_gtdbtk/run_kb_gtdbtk>`_ (third party). Note that the version may not be the most recent release.
 
 
 Hardware requirements
@@ -127,40 +126,46 @@ GTDB-Tk requires ~66G of external data that needs to be downloaded and unarchive
     tar xvzf gtdbtk_v2_data.tar.gz
 
 
-Note that different versions of the GTDB release data may not run on all versions of GTDB-Tk, below are all supported versions:
+.. note:: Note that different versions of the GTDB release data may not run on all versions of GTDB-Tk, check the supported versions!
 
 
 .. list-table::
-   :widths: 10 10 10
+   :widths: 10 10 10 20
    :header-rows: 1
 
    * - GTDB Release
      - Minimum version
      - Maximum version
-   * - R207_v2
+     - MD5
+   * - `R207_v2 <https://data.gtdb.ecogenomic.org/releases/release207/207.0/auxillary_files/gtdbtk_r207_v2_data.tar.gz>`_
      - 2.1.0
      - Current
-   * - R207
+     - df468d63265e8096d8ca01244cb95f30
+   * - `R207 <https://data.gtdb.ecogenomic.org/releases/release207/207.0/auxillary_files/gtdbtk_r207_data.tar.gz>`_
      - 2.0.0
      - 2.0.0
-   * - R202
+     - b04c55104b491f84e053a9011b36164a
+   * - `R202 <https://data.gtdb.ecogenomic.org/releases/release202/202.0/auxillary_files/gtdbtk_r202_data.tar.gz>`_
      - 1.5.0
      - 1.7.0
-   * - R95
+     - 4986526c2b935fd4dcc2e604c0322517
+   * - `R95 <https://data.gtdb.ecogenomic.org/releases/release95/95.0/auxillary_files/gtdbtk_r95_data.tar.gz>`_
      - 1.3.0
      - 1.4.2
-   * - R89
+     - 06924c63f4b555ac6fd1525b09901186
+   * - `R89 <https://data.gtdb.ecogenomic.org/releases/release89/89.0/gtdbtk_r89_data.tar.gz>`_
      - 0.3.0
      - 0.1.2
-   * - R86.2
+     - 82966ef36086237d7230955e2bfff759
+   * - `R86.2 <https://data.gtdb.ecogenomic.org/releases/release86/86.2/gtdbtk.r86_v2_data.tar.gz>`_
      - 0.2.1
      - 0.2.2
-   * - R86
+     - f71408d69fa2a289f2cdc734b7a58a02
+   * - `R86 <https://data.gtdb.ecogenomic.org/releases/release86/86.0/gtdbtk_r86_data.tar.gz>`_
      - 0.1.0
      - 0.1.6
-   * - R83
+     - d019b3541746c3673181f24e666594ba
+   * - `R83 <https://data.gtdb.ecogenomic.org/releases/release83/83.0/gtdbtk_r83_data.tar.gz>`_
      - 0.0.6
      - 0.0.7
-
-
-Reference data for prior releases of GTDB-Tk are available at: https://data.ace.uq.edu.au/public/gtdbtk
+     - 9cf523761da843b5787f591f6c5a80de