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Update of README. #170

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Feb 2, 2024
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Update of README. #170

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24c212e
draft of README changes
mikerobeson Jan 12, 2024
68bec53
updated README based on comments
mikerobeson Jan 14, 2024
9a9faa4
updated README
mikerobeson Jan 18, 2024
9f3c8c5
updated README based on comments, and added `install-prior-versions.m…
mikerobeson Jan 30, 2024
33e8aa7
fixed typos for db citation references
mikerobeson Jan 30, 2024
a81eb5f
Merge remote-tracking branch 'upstream/master' into update-readme
mikerobeson Jan 31, 2024
43e21e3
updated README install instructions
mikerobeson Feb 1, 2024
d47825f
updated install commands, moved minimal install to supplement
mikerobeson Feb 1, 2024
ac0e23f
fixed typo
mikerobeson Feb 1, 2024
98633fb
yet another typo fix
mikerobeson Feb 1, 2024
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41 changes: 35 additions & 6 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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 \
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you install 2023.7 here, but then mention 2023.9 below. Why not just use the latest?

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@mikerobeson mikerobeson Jan 14, 2024 •
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I wanted to highlight two ways to install RESCRIPt, as many of the recent versions can be installed as we've been doing. But not so with 2023.9...

I also figured, we'd not merge this PR until just before the next release anyway. This will serves as our scratch space. :-)

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okay good point, and I like the idea of keeping install instructions for pre-2023.9, but maybe we should change the header line accordingly

qiime2 q2cli q2templates q2-types q2-longitudinal q2-feature-classifier 'q2-types-genomics>2023.2' \
"pandas>=0.25.3" xmltodict ncbi-datasets-pylib
```
Expand All @@ -31,17 +31,36 @@ pip install git+https://github.com/bokulich-lab/RESCRIPt.git
```

### Option 2: Install within QIIME 2 environment
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say "before version 2023.9"?

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@mikerobeson mikerobeson Jan 18, 2024 •
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I assume the install instructions for 2024.2 are going to be largely similar to 2023.2 - 2023.7 right? That is pointing to a .../202X.Y/tested/ folder? If so, I think labelling as 'before' or 'after' 2023.9 might be confusing, as that is the only odd ball. Which is why I set it up as a note for 2023.9. 🤷 I can add the note about installing the shotgun distro too.

Also, this makes me think... should we add instructions for older versions, 2022.8 and earlier? Or would that just make things more confusing? I figure no, as folks can ask for help with older versions.

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Oh wait I forgot, pre- 2023.9 the tested folders will be https://packages.qiime2.org/qiime2/2023.7/tested/ whereas 2024.2 will be: https://packages.qiime2.org/qiime2/2024.2/amplicon/released/. So, the pre- post labeling will work. :-)

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
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RESCRIPt should now be conda installable via the same channels above, so this should not be necessary.

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Doh! 🤦


qiime rescript --help
```

#### NOTE on installing RESCRIPt within `qiime2-amplicon-2023.9`:
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I think this will already change in the next release...

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Yeah, but will this work for 2023.9 though? If not, we'll have to keep this note for that version right?

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
Expand All @@ -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)
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- [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).

Expand All @@ -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.
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**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/)