From 7335d8a50cea5fedae187f847dc4e00546b4f0c0 Mon Sep 17 00:00:00 2001 From: John Lees Date: Tue, 12 Dec 2023 10:17:40 +0000 Subject: [PATCH] Update README --- README.md | 25 ++++++++++++++++--------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index f8bbc49a..92f8e12c 100644 --- a/README.md +++ b/README.md @@ -3,15 +3,17 @@ [![Dev build Status](https://dev.azure.com/jlees/PopPUNK/_apis/build/status/johnlees.PopPUNK?branchName=master)](https://dev.azure.com/jlees/PopPUNK/_build/latest?definitionId=1&branchName=master) ![Run tests](https://github.com/bacpop/PopPUNK/workflows/Run%20tests/badge.svg) -[![Documentation Status](https://readthedocs.org/projects/poppunk/badge/?version=latest)](https://poppunk.readthedocs.io/) +[![Build and publish docs](https://github.com/bacpop/PopPUNK/actions/workflows/docs_push.yml/badge.svg)](https://github.com/bacpop/PopPUNK/actions/workflows/docs_push.yml) [![Anaconda package](https://anaconda.org/bioconda/poppunk/badges/version.svg)](https://anaconda.org/bioconda/poppunk) [![PyPI version](https://badge.fury.io/py/poppunk.svg)](https://badge.fury.io/py/poppunk) ## Description -See the [documentation](http://poppunk.readthedocs.io/en/latest/) the -[paper](https://doi.org/10.1101/gr.241455.118), and [databases](https://www.bacpop.org/poppunk/). +Links: +- [Documentation](https://poppunk.bacpop.org/) +- [Databases](https://www.bacpop.org/poppunk/) +- [Paper](https://doi.org/10.1101/gr.241455.118) If you find PopPUNK useful, please cite us: @@ -24,11 +26,11 @@ suggested methods paragraph. ## News and roadmap -The [roadmap](https://poppunk.readthedocs.io/en/latest/roadmap.html) can be found in the documentation. +The [roadmap](https://poppunk.bacpop.org/roadmap.html) can be found in the documentation. ### 2023-01-18 -We will retire the PopPUNK website. Databases have been expanded, and can be +We have retired the PopPUNK website. Databases have been expanded, and can be found here: https://www.bacpop.org/poppunk/. ### 2022-08-04 @@ -62,9 +64,9 @@ possible, you can either: ## Installation -This is for the command line version. For more details see [installation](https://poppunk.readthedocs.io/en/latest/installation.html) in the documentation. +This is for the command line version. For more details see [installation](https://poppunk.bacpop.org/installation.html) in the documentation. -There are other interfaces, in-browser and through galaxy, [detailed here](https://poppunk.net/pages/interfaces.html). +Our (beta) web interface BeeBOP is now also available: https://beebop.dide.ic.ac.uk/ ### Through conda (recommended) @@ -83,8 +85,13 @@ conda config --add channels conda-forge ## Quick usage -See the [quickstart](https://poppunk.readthedocs.io/en/latest/quickstart.html) guide -for a brief tutorial. +See the [overview](https://poppunk.bacpop.org/overview.html) first. + +Two ways of running: + +- 1) Download an [existing database](https://www.bacpop.org/poppunk/) 2) [Run assignment](https://poppunk.bacpop.org/query_assignment.html). +- OR 1) [Create sketches of input](https://poppunk.bacpop.org/sketching.html), +2) [Run QC](https://poppunk.bacpop.org/qc.html) 3) [Build a model](https://poppunk.bacpop.org/model_fitting.html). ## Docker image