From a19d106d741c3e064f6d17f2b91bf131fd28903f Mon Sep 17 00:00:00 2001 From: Mike Robeson Date: Fri, 2 Feb 2024 08:48:28 -0600 Subject: [PATCH] Update of README. (#170) --- README.md | 53 +++++++++++++--------------------- install-prior-versions.md | 60 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 79 insertions(+), 34 deletions(-) create mode 100644 install-prior-versions.md diff --git a/README.md b/README.md index c2d205e..bc0d10b 100644 --- a/README.md +++ b/README.md @@ -9,46 +9,23 @@ REference Sequence annotation and CuRatIon Pipeline RESCRIPt is a python 3 package to support a variety of operations for managing and curating reference sequence databases, DNA/RNA sequence data, and taxonomic data. See citation information below for a full benchmark and description. -## Install from source +## Install via QIIME 2. -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: +RESCRIPt is now installed as part of QIIME 2, and you can install as outlined in the [QIIME 2 Documentation](https://docs.qiime2.org/), for: + - "Shotgun Distribution" version `2023.9` and later. + - "Amplicon Distrubtion" version `2024.2` and later. -### Option 1: Minimal RESCRIPt environment: -First create a conda environment and install relevant dependencies: -``` -conda create -y -n rescript -conda activate rescript -conda install \ - -c conda-forge -c bioconda -c qiime2 -c https://packages.qiime2.org/qiime2/2023.5/tested/ -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: - -``` -pip install git+https://github.com/bokulich-lab/RESCRIPt.git -``` - -### Option 2: Install within QIIME 2 environment -First activate your QIIME 2 environment (ver 2022.8 or later) and install relevant dependencies: +### Prior versions of RESCRIPt / QIIME 2. -``` -conda activate qiime2-2023.2 -conda install -c conda-forge -c bioconda -c qiime2 -c https://packages.qiime2.org/qiime2/2023.5/tested/ -c defaults \ - xmltodict 'q2-types-genomics>2023.2' ncbi-datasets-pylib -``` -Install source: - -``` -pip install git+https://github.com/bokulich-lab/RESCRIPt.git -``` +For details on how to install prior and minimal versions of RESCRIPt for the various versions of 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: + +To view a help menu for using RESCRIPt via the QIIME 2 CLI: ``` qiime dev refresh-cache -qiime --help +qiime rescript --help ``` ## Using RESCRIPt @@ -59,10 +36,14 @@ These tutorials demonstrate some of the basic functionality of RESCRIPt, via the - [Building a COI database with BOLD sequences](https://forum.qiime2.org/t/building-a-coi-database-from-bold-references/16129) - [Building a COI database with NCBI sequences](https://forum.qiime2.org/t/building-a-coi-database-from-ncbi-references/16500) - [Using RESCRIPt's 'extract-seq-segments' to extract reference sequences without PCR primer pairs](https://forum.qiime2.org/t/using-rescripts-extract-seq-segments-to-extract-reference-sequences-without-pcr-primer-pairs/23618) +- [How to train a GTDB SSU classifier using RESCRIPt](https://forum.qiime2.org/t/how-to-train-a-gtdb-ssu-classifier-using-rescript/25725) +- [Constructing an RDP classifier](https://forum.qiime2.org/t/importing-sequence-data-with-lower-case-nucleotide-characters-constructing-an-rdp-classifier-as-an-example/25158) +- [How to train a UNITE classifier using RESCRIPt](https://forum.qiime2.org/t/how-to-train-a-unite-classifier-using-rescript/28285) 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/). @@ -79,6 +60,10 @@ RESCRIPt is released under a BSD-3-Clause license. See LICENSE for more details. However, other resources accessible via RESCRIPt are released under different licenses, as detailed below. -**The SILVA database** versions are released under different licenses. Refer to the [current SILVA release license information](https://www.arb-silva.de/silva-license-information/) for more details. +**If using the SILVA database** (*e.g.*, with `get-silva-data`): Versions are released under different licenses. Refer to the [current SILVA release license information](https://www.arb-silva.de/silva-license-information/) for more details. [How to cite SILVA](https://www.arb-silva.de/contact/). + +**If using NCBI Genbank data** (*e.g.*, with `get-ncbi-data`): See the [NCBI disclaimer and copyright notice](https://www.ncbi.nlm.nih.gov/home/about/policies/) for more details. [How to cite NCBI](https://support.nlm.nih.gov/knowledgebase/article/KA-03391/en-us). + +**If using GTDB data** (*e.g.*, with `get-gtdb-data`): See the [GTDB "about" page](https://gtdb.ecogenomic.org/about) for more details. [How to cite GTDB](https://gtdb.ecogenomic.org/about). -**If using NCBI Genbank data** (e.g., with `get-ncbi-data`): See the [NCBI disclaimer and copyright notice](https://www.ncbi.nlm.nih.gov/home/about/policies/) +**If using UNITE data** (*e.g.*, with `get-unite-data`): See the [UNITE citation page](https://unite.ut.ee/cite.php) for more details. [How to cite UNITE](https://unite.ut.ee/cite.php). diff --git a/install-prior-versions.md b/install-prior-versions.md new file mode 100644 index 0000000..c3e576c --- /dev/null +++ b/install-prior-versions.md @@ -0,0 +1,60 @@ +# 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](https://docs.qiime2.org/2023.9/install/native/#qiime-2-shotgun-distribution). You'll be able to run your RESCRIPt commands within this environment, then switch back to [qiime2-amplicon-2023.9](https://docs.qiime2.org/2023.9/install/native/#qiime-2-amplicon-distribution) 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](https://github.com/bokulich-lab/RESCRIPt/releases) 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](https://github.com/bokulich-lab/RESCRIPt/releases) and consult that version's README file for appropriate Installation instructions. \ No newline at end of file