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4 | [![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0)
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5 |
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6 | ## About Nextstrain
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7 |
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8 | **Nextstrain** is an open-source project to harness the scientific and public health potential of pathogen genome data.
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9 | 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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10 | Our goal is to aid epidemiological understanding and improve outbreak response.
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11 |
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12 | Resulting data and inferences are available live at the website [nextstrain.org](https://nextstrain.org).
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13 |
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14 | ## About Auspice
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15 |
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16 | *Definition: Observation by an augur, ie a prophetic sign.*
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17 |
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18 | **Auspice** is an open-source interactive web app for visualizing phylogenomic data.
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19 | 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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20 | Auspice may be used to explore datasets locally or run as a server to share results.
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21 |
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22 | ## Documentation
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23 |
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24 | Full documentation may be found at: [nextstrain.github.io/auspice](https://nextstrain.github.io/auspice).
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25 | The following are helpful when beginning to use Auspice:
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26 |
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27 | * [Overview of how Auspice fits together with other Nextstrain tools](https://nextstrain.org/docs/getting-started/introduction#open-source-tools-for-the-community)
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28 | * [Auspice documentation](https://nextstrain.github.io/auspice/introduction/overview)
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29 |
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30 | ## Quickstart
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31 |
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32 | ### Installation
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33 |
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34 | Install auspice for use as a global command.
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35 | This requires nodejs 10+. We recommend using a conda environment, but this is not the only way.
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36 | (See [here](https://nextstrain.github.io/auspice/introduction/install) for more installation methods & help).
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37 |
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38 | #### Install with conda (Recommended)
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39 |
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40 | Create and activate a [conda](https://docs.conda.io) environment:
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41 |
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42 | ```bash
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43 | conda create --name auspice nodejs=10
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44 | conda activate auspice
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45 | ```
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46 |
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47 | Now that the conda environment is activated, install auspice:
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48 |
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49 | ```bash
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50 | npm install --global auspice
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51 | ```
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52 |
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53 | #### Install from source
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54 |
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55 | ```bash
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56 | git clone https://github.com/nextstrain/auspice.git
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57 | cd auspice
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58 | npm install --global .
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59 | ```
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60 |
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61 | ### Obtain datasets to display
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62 |
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63 | To get up & running, you'll need datasets to visualise.
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64 | (Please see the [nextstrain docs](https://nextstrain.org/docs/) for tutorials on how to run your own analyses.)
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65 |
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66 | If you've installed auspice from `npm` you may get datasets to display via:
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67 |
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68 | ```bash
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69 | mkdir data
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70 | curl http://data.nextstrain.org/zika.json --compressed -o data/zika.json
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71 | curl http://data.nextstrain.org/ncov.json --compressed -o data/ncov.json
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72 | ...
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73 | ```
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74 |
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75 | If you've installed auspice from source, we have helper scripts to make all the datasets & narratives you see on nextstrain.org available locally:
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76 |
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77 | ```bash
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78 | # from the auspice src directory
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79 | npm run get-data
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80 | npm run get-narratives
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81 | ```
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82 |
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83 | ### Run auspice
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84 |
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85 | ```bash
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86 | auspice view --datasetDir data
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87 | ```
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88 |
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89 | And view auspice in the browser at [localhost:4000](http://localhost:4000)
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90 |
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91 | If you are editing source code, running the following command will allow hot-reloading.
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92 |
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93 | ```bash
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94 | auspice develop --datasetDir data
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95 | ```
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96 |
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97 | ### CLI (Command Line Interface)
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98 |
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99 | Run `auspice --help` or `auspice view --help` to see all the available command line options.
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100 |
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101 | ## Contributor Information
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102 |
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103 | > 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 review these resources before submitting a pull request:
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104 |
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105 | * [Contributor guide](https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md)
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106 | * [Project board with available issues](https://github.com/orgs/nextstrain/projects/5)
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107 | * [Developer docs for Auspice](./DEV_DOCS.md)
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108 |
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109 | 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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110 |
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111 | ## License and copyright
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112 |
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113 | Copyright 2014-2020 Trevor Bedford and Richard Neher.
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114 |
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115 | 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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