From 24c212e2b5ca23cc54aa8c20621179cdf7604dcc Mon Sep 17 00:00:00 2001 From: mikerobeson Date: Fri, 12 Jan 2024 15:48:58 -0600 Subject: [PATCH 1/9] draft of README changes --- README.md | 41 +++++++++++++++++++++++++++++++++++------ 1 file changed, 35 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index bec0df05..1092ca26 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ 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 \ + -c conda-forge -c bioconda -c qiime2 -c https://packages.qiime2.org/qiime2/2023.7/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 ``` @@ -31,17 +31,36 @@ 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: +First activate your QIIME 2 environment (ver `2023.2` or later) and install relevant dependencies. +The typical apporoach will be something like the command below. *Make sure the qiime version within the +http string matches the version of the active qiime environment.* ``` -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 \ +conda activate qiime2-2023.7 +conda install -c conda-forge -c bioconda -c qiime2 -c https://packages.qiime2.org/qiime2/2023.7/tested/ -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 +``` + +#### NOTE on installing RESCRIPt within `qiime2-amplicon-2023.9`: +As the QIIME 2 team is still refining some details on how the the various distributions +of QIIME 2 wil be handled (*i.e.* `qiime2-amplicon-2023.9`, `qiime2-shotgun-2023.9`), you'll have to +install RESCIPt like so: +``` +conda activate qiime2-amplicon-2023.9 +conda install -c conda-forge -c bioconda -c qiime2 \ +-c https://packages.qiime2.org/qiime2/2023.9/shotgun/released/ \ +-c defaults xmltodict 'q2-types-genomics>2023.5' ncbi-datasets-pylib + +pip install git+https://github.com/bokulich-lab/RESCRIPt.git + +qiime rescript --help ``` ### Read help documentation @@ -59,6 +78,9 @@ 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). @@ -79,6 +101,13 @@ 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. + +**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. + +**If using GTDB data** (*e.g.*, with `get-gtdb-data`): See the [GTDB "about" page](https://gtdb.ecogenomic.org/about) for more details. + +**If using UNITE data** (*e.g.*, with `get-unite-data`): See the [UNITE citation page](https://unite.ut.ee/cite.php) for more details. + +**If importing and processing RDP data**: See both the [RDP Staff GitHub page](https://github.com/rdpstaff) and the [RDP SourceForge page](https://sourceforge.net/projects/rdp-classifier/) for more details. -**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/) From 68bec532e078aab6083b2cbf6a980f594254c727 Mon Sep 17 00:00:00 2001 From: mikerobeson Date: Sun, 14 Jan 2024 15:22:55 -0600 Subject: [PATCH 2/9] updated README based on comments --- README.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/README.md b/README.md index 1092ca26..5f374a53 100644 --- a/README.md +++ b/README.md @@ -108,6 +108,3 @@ However, other resources accessible via RESCRIPt are released under different li **If using GTDB data** (*e.g.*, with `get-gtdb-data`): See the [GTDB "about" page](https://gtdb.ecogenomic.org/about) for more details. **If using UNITE data** (*e.g.*, with `get-unite-data`): See the [UNITE citation page](https://unite.ut.ee/cite.php) for more details. - -**If importing and processing RDP data**: See both the [RDP Staff GitHub page](https://github.com/rdpstaff) and the [RDP SourceForge page](https://sourceforge.net/projects/rdp-classifier/) for more details. - From 9a9faa4b11ef1a99bb305b0f4c48ff5e2bcd6fa7 Mon Sep 17 00:00:00 2001 From: mikerobeson Date: Thu, 18 Jan 2024 10:24:33 -0600 Subject: [PATCH 3/9] updated README --- README.md | 61 ++++++++++++++++++++++++++++++++++++++++++------------- 1 file changed, 47 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index 5f374a53..dcb0fce8 100644 --- a/README.md +++ b/README.md @@ -20,25 +20,29 @@ 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/qiime2/2023.7/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 + -c conda-forge -c bioconda -c qiime2 \ + -c https://packages.qiime2.org/qiime2/2024.2/amplicon/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 + +qiime rescript --help ``` -### Option 2: Install within QIIME 2 environment -First activate your QIIME 2 environment (ver `2023.2` or later) and install relevant dependencies. +### Option 2: Install within QIIME 2 environments `2024.2` and later. +First activate your QIIME 2 environment and install relevant dependencies. The typical apporoach will be something like the command below. *Make sure the qiime version within the http string matches the version of the active qiime environment.* ``` -conda activate qiime2-2023.7 -conda install -c conda-forge -c bioconda -c qiime2 -c https://packages.qiime2.org/qiime2/2023.7/tested/ -c defaults \ - xmltodict 'q2-types-genomics>2023.2' ncbi-datasets-pylib +conda activate qiime2-amplicon-2024.2 +conda install -c conda-forge -c bioconda -c qiime2 \ + -c https://packages.qiime2.org/qiime2/2024.2/amplicon/tested/ \ + -c defaults xmltodict 'q2-types-genomics>2023.2' ncbi-datasets-pylib ``` Install source: @@ -48,21 +52,50 @@ pip install git+https://github.com/bokulich-lab/RESCRIPt.git qiime rescript --help ``` -#### NOTE on installing RESCRIPt within `qiime2-amplicon-2023.9`: -As the QIIME 2 team is still refining some details on how the the various distributions -of QIIME 2 wil be handled (*i.e.* `qiime2-amplicon-2023.9`, `qiime2-shotgun-2023.9`), you'll have to -install RESCIPt like so: +### Option 3: Older versions of QIIME 2 & RESCRIPt + +#### Install within the QIIME 2 `2023.9` environment: + +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` using 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/released/ \ --c defaults xmltodict 'q2-types-genomics>2023.5' ncbi-datasets-pylib + -c https://packages.qiime2.org/qiime2/2023.9/shotgun/released/ \ + -c defaults xmltodict 'q2-types-genomics>2023.5' ncbi-datasets-pylib +``` + +Install source: + +``` +pip install git+https://github.com/bokulich-lab/RESCRIPt.git + +qiime rescript --help +``` + + +#### Install within QIIME 2 environments `2023.2` - `2023.7`. +First activate your QIIME 2 environment and install relevant dependencies. +The typical apporoach will be something like the command below. *Make sure the qiime version within the +http string matches the version of the active qiime environment.* + +``` +conda activate qiime2-2023.7 +conda install -c conda-forge -c bioconda -c qiime2 \ + -c https://packages.qiime2.org/qiime2/2023.7/tested/ \ + -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. + ### Read help documentation To view a help menu for using rescript via the QIIME 2 CLI: ``` From 9f3c8c57ef16a8625118c34b1cb0a4d0ad4e1a31 Mon Sep 17 00:00:00 2001 From: mikerobeson Date: Tue, 30 Jan 2024 15:36:03 -0600 Subject: [PATCH 4/9] updated README based on comments, and added `install-prior-versions.md` document. --- README.md | 59 ++++++--------------------------------- install-prior-versions.md | 45 +++++++++++++++++++++++++++++ 2 files changed, 54 insertions(+), 50 deletions(-) create mode 100644 install-prior-versions.md diff --git a/README.md b/README.md index dcb0fce8..4256a0a3 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,7 @@ 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/tested/ \ + -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 ``` @@ -34,55 +34,14 @@ qiime rescript --help ``` ### Option 2: Install within QIIME 2 environments `2024.2` and later. -First activate your QIIME 2 environment and install relevant dependencies. -The typical apporoach will be something like the command below. *Make sure the qiime version within the +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.* ``` conda activate qiime2-amplicon-2024.2 -conda install -c conda-forge -c bioconda -c qiime2 \ - -c https://packages.qiime2.org/qiime2/2024.2/amplicon/tested/ \ - -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 -``` - -### Option 3: Older versions of QIIME 2 & RESCRIPt - -#### Install within the QIIME 2 `2023.9` environment: - -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` using 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/released/ \ - -c defaults xmltodict 'q2-types-genomics>2023.5' ncbi-datasets-pylib -``` - -Install source: - -``` -pip install git+https://github.com/bokulich-lab/RESCRIPt.git - -qiime rescript --help -``` - - -#### Install within QIIME 2 environments `2023.2` - `2023.7`. -First activate your QIIME 2 environment and install relevant dependencies. -The typical apporoach will be something like the command below. *Make sure the qiime version within the -http string matches the version of the active qiime environment.* - -``` -conda activate qiime2-2023.7 conda install -c conda-forge -c bioconda -c qiime2 \ - -c https://packages.qiime2.org/qiime2/2023.7/tested/ \ + -c https://packages.qiime2.org/qiime2/2024.2/amplicon/passed/ \ -c defaults xmltodict 'q2-types-genomics>2023.2' ncbi-datasets-pylib ``` Install source: @@ -93,8 +52,8 @@ 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. +### Prior versions of RESCRIPt. +For details on how to install prior versions of RESCRIPt, please see the `install-prior-versions.md` document. ### Read help documentation To view a help menu for using rescript via the QIIME 2 CLI: @@ -134,10 +93,10 @@ 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. -**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. +**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/) in your work. -**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. +**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) in your work. -**If using GTDB data** (*e.g.*, with `get-gtdb-data`): See the [GTDB "about" page](https://gtdb.ecogenomic.org/about) for more details. +**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) in your work. -**If using UNITE data** (*e.g.*, with `get-unite-data`): See the [UNITE citation page](https://unite.ut.ee/cite.php) for more details. +**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)) in your work. diff --git a/install-prior-versions.md b/install-prior-versions.md new file mode 100644 index 00000000..ca62f423 --- /dev/null +++ b/install-prior-versions.md @@ -0,0 +1,45 @@ +# How to install prior versions of RESCRIPt. + +## 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 +``` + +Install source: + +``` +pip install git+https://github.com/bokulich-lab/RESCRIPt.git + +qiime rescript --help +``` + + +## Install within the QIIME 2 releases `2023.2` - `2023.7`. +The typical apporoach will be something like the command below. *Make sure the qiime version within the http string matches the version of the active qiime environment.* + +``` +conda activate qiime2-2023.7 + +conda install -c conda-forge -c bioconda -c qiime2 \ + -c https://packages.qiime2.org/qiime2/2023.7/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 From 33e8aa72b8d58e5872b0db76e2b15de0c66c17ea Mon Sep 17 00:00:00 2001 From: mikerobeson Date: Tue, 30 Jan 2024 15:39:10 -0600 Subject: [PATCH 5/9] fixed typos for db citation references --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 4256a0a3..f9c88235 100644 --- a/README.md +++ b/README.md @@ -93,10 +93,10 @@ 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. -**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/) in your work. +**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) in your work. +**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) in your work. +**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 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)) in your work. +**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). From 43e21e3ba6c4e22039e5df4194edeeb91c24c969 Mon Sep 17 00:00:00 2001 From: mikerobeson Date: Thu, 1 Feb 2024 12:55:35 -0600 Subject: [PATCH 6/9] updated README install instructions --- README.md | 46 ++++++++++++++++++++-------------------------- 1 file changed, 20 insertions(+), 26 deletions(-) diff --git a/README.md b/README.md index d4326d7a..f711f87c 100644 --- a/README.md +++ b/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/). From d47825f8cecd903c6240f43b17fe9cd0aaa81e2d Mon Sep 17 00:00:00 2001 From: mikerobeson Date: Thu, 1 Feb 2024 15:30:02 -0600 Subject: [PATCH 7/9] updated install commands, moved minimal install to supplement --- README.md | 41 +++++++------------------------------ install-prior-versions.md | 43 ++++++++++++++++++++++++++------------- 2 files changed, 36 insertions(+), 48 deletions(-) diff --git a/README.md b/README.md index f711f87c..9c4a7f59 100644 --- a/README.md +++ b/README.md @@ -9,50 +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 the QIIME 2, 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: Installed as part of a QIIME 2 distribution. - -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. - -### Option 2: Minimal RESCRIPt environment - -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 -``` - -Install source: - -``` -pip install git+https://github.com/bokulich-lab/RESCRIPt.git - -qiime rescript --help -``` ### 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. +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 diff --git a/install-prior-versions.md b/install-prior-versions.md index ca62f423..c3e576c9 100644 --- a/install-prior-versions.md +++ b/install-prior-versions.md @@ -1,36 +1,51 @@ -# How to install prior versions of RESCRIPt. +# How to install other versions of RESCRIPt. -## Install within the QIIME 2 `2023.9` release: +## 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: -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. +First create a conda environment and install relevant dependencies using either `conda` or `mamba`. -It is possible to install RESCRIPt within `qiime2-amplicon-2023.9`. YOu can try via the following commands: +*Note: update `{ENV_VERSION}` in the commands below to match the QIIME 2 release.* ``` -conda activate qiime2-amplicon-2023.9 +conda create -y -n rescript +conda activate rescript -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 +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 source: +## 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: ``` -pip install git+https://github.com/bokulich-lab/RESCRIPt.git +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`. -The typical apporoach will be something like the command below. *Make sure the qiime version within the http string matches the version of the active qiime environment.* +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 qiime2-2023.7 +conda activate qiime2-{ENV_VERSION} conda install -c conda-forge -c bioconda -c qiime2 \ - -c https://packages.qiime2.org/qiime2/2023.7/passed/ \ + -c https://packages.qiime2.org/qiime2/{ENV_VERSION}/passed/ \ -c defaults xmltodict 'q2-types-genomics>2023.2' ncbi-datasets-pylib ``` Install source: From ac0e23f5a092a8dde6e8e849d9861fa09c40e5ec Mon Sep 17 00:00:00 2001 From: mikerobeson Date: Thu, 1 Feb 2024 15:36:38 -0600 Subject: [PATCH 8/9] fixed typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9c4a7f59..dea8e13e 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ RESCRIPt is a python 3 package to support a variety of operations for managing a ## Install via QIIME 2. -RESCRIPt is now installed as part of the QIIME 2, as outlined in the [QIIME 2 Documentation](https://docs.qiime2.org/), for: +RESCRIPt is now installed as part of QIIME 2, 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. From 98633fb5c22fbbf11576a95cc74d89f827bf62e8 Mon Sep 17 00:00:00 2001 From: mikerobeson Date: Thu, 1 Feb 2024 15:38:21 -0600 Subject: [PATCH 9/9] yet another typo fix --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index dea8e13e..bc0d10bb 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ RESCRIPt is a python 3 package to support a variety of operations for managing a ## Install via QIIME 2. -RESCRIPt is now installed as part of QIIME 2, as outlined in the [QIIME 2 Documentation](https://docs.qiime2.org/), for: +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.