From d4f33f08c441c280e28cc1e327c0f9c22cfcf3c7 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Fri, 19 Jan 2024 14:06:38 -0800 Subject: [PATCH 1/2] Add Quickstart section to the top level README MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Requested internally by @trvrb to point to add a Quickstart section to point people to the primary workflow of the repo.¹ ¹ https://bedfordlab.slack.com/archives/C0KQCN813/p1705696505953639 --- README.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/README.md b/README.md index ee1a6e6..9262fad 100644 --- a/README.md +++ b/README.md @@ -7,6 +7,17 @@ This repository contains two workflows for the analysis of Zika virus data: Each folder contains a README.md with more information. +## Quickstart + +Follow the [standard installation instructions](https://docs.nextstrain.org/page/install.html) for Nextstrain's suite of software tools. + +Then run the default phylogenetic workflow via: +``` +cd phylogenetic/ +nextstrain build . +nextstrain view . +``` + ## Documentation - [Contributor documentation](./CONTRIBUTING.md) From 85dd505b7eb1038def962541ad29ebe4b101519c Mon Sep 17 00:00:00 2001 From: Trevor Bedford Date: Fri, 19 Jan 2024 14:47:40 -0800 Subject: [PATCH 2/2] Further updates to READMEs 1. Installation section in top-level readme (I'm always looking for this) 2. Make it clearer that phylogenetic workflow needs to be run from within the phylogenetic/ directory --- README.md | 13 ++++++++----- phylogenetic/README.md | 22 +++++++++++++--------- 2 files changed, 21 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index 9262fad..b3c7fb0 100644 --- a/README.md +++ b/README.md @@ -3,15 +3,17 @@ This repository contains two workflows for the analysis of Zika virus data: - [`ingest/`](./ingest) - Download data from GenBank, clean and curate it and upload it to S3 -- [`phylogenetic/`](./phylogenetic) - Make phylogenetic trees for nextstrain.org +- [`phylogenetic/`](./phylogenetic) - Filter sequences, align, construct phylogeny and export for visualization -Each folder contains a README.md with more information. +Each folder contains a README.md with more information. The results of running both workflows are publicly visible at [nextstrain.org/zika](https://nextstrain.org/zika). -## Quickstart +## Installation + +Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html) for Nextstrain's suite of software tools. -Follow the [standard installation instructions](https://docs.nextstrain.org/page/install.html) for Nextstrain's suite of software tools. +## Quickstart -Then run the default phylogenetic workflow via: +Run the default phylogenetic workflow via: ``` cd phylogenetic/ nextstrain build . @@ -20,4 +22,5 @@ nextstrain view . ## Documentation +- [Running a pathogen workflow](https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html) - [Contributor documentation](./CONTRIBUTING.md) diff --git a/phylogenetic/README.md b/phylogenetic/README.md index 5d831e7..2f6b082 100644 --- a/phylogenetic/README.md +++ b/phylogenetic/README.md @@ -5,7 +5,8 @@ This is the [Nextstrain](https://nextstrain.org) build for Zika, visible at ## Software requirements -Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html) for Nextstrain's suite of software tools. +Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html) +for Nextstrain's suite of software tools. ## Usage @@ -13,30 +14,33 @@ If you're unfamiliar with Nextstrain builds, you may want to follow our [Running a Pathogen Workflow guide][] first and then come back here. The easiest way to run this pathogen build is using the Nextstrain -command-line tool: +command-line tool from within the `phylogenetic/` directory: + cd phylogenetic/ nextstrain build . Build output goes into the directories `data/`, `results/` and `auspice/`. -Once you've run the build, you can view the results in auspice: +Once you've run the build, you can view the results with: - nextstrain view auspice/ + nextstrain view . ## Configuration -Configuration takes place entirely with the `Snakefile`. This can be read top-to-bottom, each rule -specifies its file inputs and output and also its parameters. There is little redirection and each -rule should be able to be reasoned with on its own. +Configuration takes place entirely with the `Snakefile`. This can be read +top-to-bottom, each rule specifies its file inputs and output and also its +parameters. There is little redirection and each rule should be able to be +reasoned with on its own. ### Using GenBank data -This build starts by pulling preprocessed sequence and metadata files from: +This build starts by pulling preprocessed sequence and metadata files from: * https://data.nextstrain.org/files/zika/sequences.fasta.zst * https://data.nextstrain.org/files/zika/metadata.tsv.zst -The above datasets have been preprocessed and cleaned from GenBank and are updated at regular intervals. +The above datasets have been preprocessed and cleaned from GenBank using the +[ingest/](../ingest/) workflow and are updated at regular intervals. ### Using example data