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* readme-dev-docs-reorg: Improve findability of documentation Gather dev docs pointers in one place Default to the global contributor guide for all nextstrain projects
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| # Development docs | ||
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| ## Getting started | ||
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| Thank you for helping us to improve Nextstrain! | ||
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| ##### [To get started, please see the contributing guide for useful information about how to pick an issue, submit your contributions, and so on.](https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md) | ||
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| This project strictly adheres to the [Contributor Covenant Code of Conduct](https://github.com/nextstrain/.github/blob/master/CODE_OF_CONDUCT.md). | ||
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| Please see the [project board](https://github.com/orgs/nextstrain/projects/5) for currently available issues. | ||
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| ## Contributing code | ||
| [Please see the main auspice docs](https://nextstrain.github.io/auspice/introduction/install) for details on how to install and run auspice locally. | ||
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| For pull requests, please use [eslint](https://eslint.org/) as much as possible -- thanks! | ||
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| ## Contributing to Documentation | ||
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| This documentation is all contained within the Auspice GitHub repo -- see [the README](https://github.com/nextstrain/auspice/tree/master/docs-src) within the `docs-src` directory for more details and instructions on how to contribute. | ||
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| Please see [docs-src/README](./docs-src/README.md) for how the auspice documentation site is built. | ||
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| 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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| ## Releases & versioning | ||
| 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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| [](https://www.npmjs.com/package/auspice) | ||
| [](https://www.gnu.org/licenses/agpl-3.0) | ||
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| ## About Nextstrain | ||
| Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. | ||
| We provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread. | ||
| Our goal is to aid epidemiological understanding and improve outbreak response. | ||
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| Resulting data and inferences are available live at the website [nextstrain.org](https://nextstrain.org). | ||
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| > We have received a number of generous offers to contribute developer effort to nextstrain (and auspice) following our work on [hCoV-19](https://nextstrain.org/ncov). | ||
| We are flattered and would welcome contributions! | ||
| Please see the [contributing](./CONTRIBUTING.md) documentation for more details. | ||
| A list of potential issues is being actively maintained at https://github.com/orgs/nextstrain/projects | ||
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| # Auspice | ||
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| ## About Auspice | ||
| *Definition: Observation by an augur, ie a prophetic sign.* | ||
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| Auspice is an open-source interactive web app for visualizing phylogenomic data. | ||
| It may be used in tandem with nextstrain's bioinformatics toolkit [augur](https://github.com/nextstrain/augur) or on its own. | ||
| Auspice may be used to explore datasets locally or run as a as a server to share results. | ||
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| ## Documentation | ||
| * [Overview of how Auspice fits together with other Nextstrain tools](https://nextstrain.org/docs/getting-started/introduction#open-source-tools-for-the-community) | ||
| * [Auspice documentation](https://nextstrain.github.io/auspice/introduction/overview) | ||
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| **Please see [nextstrain.github.io/auspice](https://nextstrain.github.io/auspice) for auspice documentation.** | ||
| > We have received a number of generous offers to contribute developer effort to nextstrain (and auspice) following our work on hCoV-19. We welcome contributions! To get started, please see these resources: | ||
| * [Contributor guide](https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md) | ||
| * [Project board with available issues](https://github.com/orgs/nextstrain/projects/5) | ||
| * [Developer docs for Auspice](./DEV_DOCS.md) | ||
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| ## Quickstart | ||
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| ## Quickstart | ||
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| #### Installation | ||
| ### Installation | ||
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| Install auspice for use as a global command. | ||
| This requires nodejs 10+. We recommend using a conda environment, but this is not the only way. | ||
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| (See [here](https://nextstrain.github.io/auspice/introduction/install) for more installation methods & help). | ||
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| #### Obtain datasets to display: | ||
| ### Obtain datasets to display: | ||
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| In order to get up & running you'll need datasets to visualise. | ||
| (Please see the [nextstrain docs](https://nextstrain.org/docs/) for tutorials on how to run your own analyses.) | ||
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| npm run get-narratives | ||
| ``` | ||
| #### Run auspice: | ||
| ### Run auspice: | ||
| ```bash | ||
| auspice view --datasetDir data | ||
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| Full documentation may be found at: [nextstrain.github.io/auspice](https://nextstrain.github.io/auspice). | ||
| ## Development, comments, issues and bugs | ||
| Auspice is developed via GitHub and issues are very welcome. Alternatively, [email us](mailto:[email protected]) with any questions or comments you may have. | ||
| If you are interested in submitting a pull request please use [eslint](https://eslint.org/) as much as possible -- thanks! | ||
| 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). | ||
| Please see [docs-src/README](./docs-src/README.md) for how the auspice documentation site is built. | ||
| > 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). | ||
| ## License and copyright | ||
| Copyright 2014-2019 Trevor Bedford and Richard Neher. | ||
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