| 1 | [](https://travis-ci.com/nextstrain/auspice)
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| 2 | [](https://www.npmjs.com/package/auspice)
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| 3 | [](https://www.gnu.org/licenses/agpl-3.0)
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| 4 |
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| 5 |
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| 6 | Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data.
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| 7 | We provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread.
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| 8 | Our goal is to aid epidemiological understanding and improve outbreak response.
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| 9 |
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| 10 | Resulting data and inferences are available live at the website [nextstrain.org](https://nextstrain.org).
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| 11 |
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| 12 | # Auspice
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| 13 |
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| 14 | *Definition: Observation by an augur, ie a prophetic sign.*
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| 15 |
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| 16 | Auspice is an open-source interactive web app for visualizing phylogenomic data.
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| 17 | It may be used in tandem with nextstrain's bioinformatics toolkit [augur](https://github.com/nextstrain/augur) or on its own.
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| 18 | Auspice may be used to explore datasets locally or run as a as a server to share results.
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| 19 |
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| 20 | ## Documentation
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| 21 |
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| 22 | **Please see [nextstrain.github.io/auspice](https://nextstrain.github.io/auspice) for auspice documentation.**
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| 23 |
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| 24 |
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| 25 | ## Installation
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| 26 |
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| 27 | ```bash
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| 28 | npm install --global auspice
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| 29 | ```
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| 30 |
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| 31 | See [here](https://nextstrain.github.io/auspice/introduction/install) for full instructions, including how to install from source.
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| 32 |
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| 33 |
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| 34 | ## Quickstart
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| 35 |
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| 36 | In order to get up & running you'll need to have some datasets to visualise.
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| 37 | Please see the [nextstrain docs](https://nextstrain.org/docs/) for tutorials on how to do this.
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| 38 | For the purposes of getting started, you can download the current zika dataset via:
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| 39 |
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| 40 | ```
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| 41 | mkdir datasets
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| 42 | curl http://data.nextstrain.org/zika.json --compressed -o datasets/zika.json
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| 43 | ```
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| 44 |
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| 45 | And then run `auspice` via:
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| 46 | ```
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| 47 | auspice view --datasetDir datasets
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| 48 | ```
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| 49 | This will allow you to run auspice locally (i.e. from your computer) and view the dataset which is behind [nextstrain.org/zika](https://nextstrain.org/zika).
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| 50 |
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| 51 |
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| 52 | Run `auspice --help` or visit [nextstrain.github.io/auspice](https://nextstrain.github.io/auspice) for more information.
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| 53 |
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| 54 | ## Development, comments, issues and bugs
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| 55 |
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| 56 | Auspice is developed via GitHub and issues are very welcome. Alternatively, [email us](mailto:hello@nextstrain.org) with any questions or comments you may have.
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| 57 | If you are interested in submitting a pull request please use [eslint](https://eslint.org/) as much as possible -- thanks!
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| 58 |
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| 59 | New versions are released via the `./releaseNewVersion.sh` script from an up-to-date `master` branch. It will prompt you for the version number increase, push changes to the `release` branch and, as long as Travis-CI is successful then a new version will be automatically published to [npm](https://www.npmjs.com/package/auspice).
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| 60 |
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| 61 | Please see [docs-src/README](./docs-src/README.md) for how the auspice documentation site is built.
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| 62 |
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| 63 | > Note that currently the documentation must be rebuilt & pushed to GitHub _after_ a new version is released in order for the changelog to correctly appear at [nextstrain.github.io/auspice/releases/changelog](https://nextstrain.github.io/auspice/releases/changelog).
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| 64 |
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| 65 |
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| 66 | ## License and copyright
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| 67 | Copyright 2014-2019 Trevor Bedford and Richard Neher.
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| 68 |
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| 69 | Source code to Nextstrain is made available under the terms of the [GNU Affero General Public License](LICENSE.txt) (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
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