From 83ebb175da07176f77895f2dcdebfcbaa63780af Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 11 Aug 2024 11:09:37 -0700 Subject: [PATCH 1/2] update plugin documentation for users --- doc/command-line.md | 30 +++++++++++++++++++++++++++--- doc/dev_plugins.md | 2 +- 2 files changed, 28 insertions(+), 4 deletions(-) diff --git a/doc/command-line.md b/doc/command-line.md index 63ee87d368..66f7aa941e 100644 --- a/doc/command-line.md +++ b/doc/command-line.md @@ -2324,7 +2324,7 @@ fast selection and lazy loading of sketches in many situations. The `sig check` command can also be used to create standalone manifests from collections using a picklist, with the `-m/--save-manifest-matching` option. This is useful for commands that don't support picklists natively, -e.g. plugins and extensions. +such as commands in plugins. Note that `sig collect` and `sig check` will generate manifests containing the pathnames given to them - so if you use relative paths, the references @@ -2345,7 +2345,7 @@ file. You can read more about the details of zip files and manifests in [the advanced usage information for databases](databases-advanced.md). -### Using sourmash plugins +## Using sourmash plugins As of sourmash v4.7.0, sourmash has an experimental plugins interface! The plugin interface supports extending sourmash to load and save @@ -2359,4 +2359,28 @@ is installed in. In the future, we will include a list of available sourmash plugins in the documentation, and also provide a way to list available plugins. -You can list all installed plugins with `sourmash info -v`. +You can list all installed plugins and their versions with `sourmash info -v`. + +Below are some useful plugins that the sourmash team uses regularly +and supports! + +### The `branchwater` plugin - multithreaded and optimized sourmash operations + +(Installable via conda and pip as `sourmash_plugin_branchwater`.) + +The +[`branchwater` plugin](https://github.com/sourmash-bio/sourmash_plugin_branchwater) +provides faster and lower memory versions of `search`, `gather`, and +`sketch`, as well as large-scale metagenome search +(used for [petabyte-scale sequence search](https://www.biorxiv.org/content/10.1101/2022.11.02.514947v1)) +and large-scale clustering. + +Read [the branchwater plugin docs](https://github.com/sourmash-bio/sourmash_plugin_branchwater/tree/main/doc/) for more information, and ask questions on [the sourmash issue tracker!](https://github.com/dib-lab/sourmash/issues) + +### The `betterplot` plugin - improved plotting and visualization + +(Installable via pip as `sourmash_plugin_betterplot`.) + +The [`betterplot` plugin](https://github.com/sourmash-bio/sourmash_plugin_betterplot/) provides a variety of new plotting outputs for sourmash, including improved distance matrices, MDS plots, tSNE plots, upset plots, and Venn diagrams. It also supports cluster-cutting and extraction, as well as improved labeling and coloring by category. + +Read [the betterplot docs](https://github.com/sourmash-bio/sourmash_plugin_betterplot/) for more information, and ask questions on [the sourmash issue tracker!](https://github.com/dib-lab/sourmash/issues). diff --git a/doc/dev_plugins.md b/doc/dev_plugins.md index 136e882308..f1a4ef6381 100644 --- a/doc/dev_plugins.md +++ b/doc/dev_plugins.md @@ -69,7 +69,7 @@ Some (early stage) plugins are also available as examples: ## Debugging plugins -`sourmash info -v` will list all installed plugins. +`sourmash info -v` will list all installed plugins and their versions. `sourmash sig cat -o ` is a simple way to invoke a `save_to` plugin. Use `-d` to turn on debugging output. From ea22c6d7e6774f5885f463da5d0ec76dc8802240 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Sun, 11 Aug 2024 18:21:24 -0700 Subject: [PATCH 2/2] Apply suggestions from code review Co-authored-by: Luiz Irber --- doc/command-line.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/command-line.md b/doc/command-line.md index 66f7aa941e..05f7414753 100644 --- a/doc/command-line.md +++ b/doc/command-line.md @@ -2375,7 +2375,7 @@ provides faster and lower memory versions of `search`, `gather`, and (used for [petabyte-scale sequence search](https://www.biorxiv.org/content/10.1101/2022.11.02.514947v1)) and large-scale clustering. -Read [the branchwater plugin docs](https://github.com/sourmash-bio/sourmash_plugin_branchwater/tree/main/doc/) for more information, and ask questions on [the sourmash issue tracker!](https://github.com/dib-lab/sourmash/issues) +Read [the branchwater plugin docs](https://github.com/sourmash-bio/sourmash_plugin_branchwater/tree/main/doc/) for more information, and ask questions on [the sourmash issue tracker!](https://github.com/sourmash-bio/sourmash/issues) ### The `betterplot` plugin - improved plotting and visualization @@ -2383,4 +2383,4 @@ Read [the branchwater plugin docs](https://github.com/sourmash-bio/sourmash_plug The [`betterplot` plugin](https://github.com/sourmash-bio/sourmash_plugin_betterplot/) provides a variety of new plotting outputs for sourmash, including improved distance matrices, MDS plots, tSNE plots, upset plots, and Venn diagrams. It also supports cluster-cutting and extraction, as well as improved labeling and coloring by category. -Read [the betterplot docs](https://github.com/sourmash-bio/sourmash_plugin_betterplot/) for more information, and ask questions on [the sourmash issue tracker!](https://github.com/dib-lab/sourmash/issues). +Read [the betterplot docs](https://github.com/sourmash-bio/sourmash_plugin_betterplot/) for more information, and ask questions on [the sourmash issue tracker!](https://github.com/sourmash-bio/sourmash/issues).