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Add Quickstart section to the top level README #30

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Jan 20, 2024
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Add Quickstart section to the top level README #30

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Add Quickstart section to the top level README
joverlee521 Jan 19, 2024
85dd505
Further updates to READMEs
trvrb Jan 19, 2024
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18 changes: 16 additions & 2 deletions README.md
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Expand Up @@ -3,10 +3,24 @@
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).

## Installation

Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html) for Nextstrain's suite of software tools.

## Quickstart

Run the default phylogenetic workflow via:
```
cd phylogenetic/
nextstrain build .
nextstrain view .
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This could be two lines as well:

Suggested change
cd phylogenetic/
nextstrain build .
nextstrain view .
nextstrain build phylogenetic/
nextstrain view phylogenetic/

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@trvrb trvrb Jan 19, 2024 •
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Cool! I think I might prefer the 3-line cd version as https://github.com/nextstrain/zika/blob/main/phylogenetic/README.md seems to be suggesting to run from within phylogenetics/ directory. (However, realize now that this actually needs to be spelled out in that readme). Basically expecting Quickstart to not deviate too heavily from the longer version of Usage.

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I just added a note on this here https://github.com/nextstrain/zika/pull/30/files#diff-0442ef409a305d27ae6b86f4cd48a1cf192e966cc8cf2e2da016fd63375408fbR17

```

## Documentation

- [Running a pathogen workflow](https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html)
- [Contributor documentation](./CONTRIBUTING.md)
22 changes: 13 additions & 9 deletions phylogenetic/README.md
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Expand Up @@ -5,38 +5,42 @@ 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

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

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