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1 | 1 |  |
2 | 2 |
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3 | | -# jbrowse-plugin-my-project |
| 3 | +# jbrowse-plugin-quantseq |
4 | 4 |
|
5 | | -> Template to quickly start a new JBrowse plugin |
| 5 | +This is an external plugin for the [JBrowse 2](https://jbrowse.org/jb2/) |
| 6 | +open-source platform for visualizing and integrating biological data. |
| 7 | +This plugin implements a QuantitativeSequence (quantseq) track type. It builds on the concept of a "dynamic sequence (dynseq)" track that was added to the |
| 8 | +awesome [WashU Epigenome Browser](http://epigenomegateway.wustl.edu/). |
6 | 9 |
|
7 | | -## Usage |
| 10 | +This track combines the QuantitativeTrack and the ReferenceSequenceTrack from |
| 11 | +JBrowse 2 in order to visualize quantitative data for regulatory genomics at |
| 12 | +base-resolution, such as the predictions of the [BPNet](https://github.com/kundajelab/bpnet) model. Here is what this new track looks like: |
8 | 13 |
|
9 | | -You can use this template to create a new GitHub repository or a new local |
10 | | -project. |
11 | 14 |
|
12 | | -### Software requirements |
| 15 | +## Contributing |
13 | 16 |
|
14 | | -- [git](https://git-scm.com/downloads) |
15 | | -- [Node.js](https://nodejs.org/en/download/) (version 10 or greater) |
16 | | -- [yarn](https://yarnpkg.com/en/docs/install) (or npm which comes with Node.js) |
17 | | - |
18 | | -### Create a new project from this template |
19 | | - |
20 | | -You can click the "Use this template" button in the repository (instructions |
21 | | -[here](https://docs.github.com/en/free-pro-team@latest/github/creating-cloning-and-archiving-repositories/creating-a-repository-from-a-template)): |
22 | | - |
23 | | - |
24 | | - |
25 | | -Or you can use the GitHub CLI: |
26 | | - |
27 | | -```console |
28 | | -$ gh repo create jbrowse-plugin-my-project --template https://github.com/GMOD/jbrowse-plugin-template.git |
29 | | -``` |
30 | | - |
31 | | -Or you can start a plugin locally: |
32 | | - |
33 | | -```console |
34 | | -$ git clone https://github.com/GMOD/jbrowse-plugin-template.git jbrowse-plugin-my-project |
35 | | -$ cd jbrowse-plugin-my-project |
36 | | -$ rm -rf .git |
37 | | -$ # If you want to use Git, re-initialize it |
38 | | -$ git init |
39 | | -``` |
40 | | - |
41 | | -## Getting started |
42 | | - |
43 | | -### Setup |
44 | | - |
45 | | -Run `yarn init` (or `npm init`) and answer the prompts to fill out the |
46 | | -information for your plugin |
47 | | - |
48 | | -- Make sure you at least enter a "name" (probably starting with |
49 | | - "jbrowse-plugin-", or "@myscope/jbrowse-plugin-" if you're going to publish to |
50 | | - an NPM organization) |
51 | | -- Other fields may be left blank |
52 | | -- leave the "entry point" as `dist/index.js` |
53 | | - |
54 | | -Now run `yarn` (or `rm yarn.lock && npm install` to use npm instead of yarn) to install the necessary dependencies. |
55 | | - |
56 | | -After this, run `yarn setup` (or `npm run setup`). |
57 | | -This configures your project, and adds a build of JBrowse 2 that can be used to test your plugin during development. |
58 | | - |
59 | | -### Build |
60 | | - |
61 | | -```console |
62 | | -$ yarn build ## or `npm run build` |
63 | | -``` |
64 | | - |
65 | | -### Development |
66 | | - |
67 | | -To develop against JBrowse Web: |
68 | | - |
69 | | -- Start a development version of JBrowse Web (see |
70 | | - [here](https://github.com/GMOD/jbrowse-components/blob/master/CONTRIBUTING.md)) |
71 | | -- In this project, run `yarn start` (or `npm run start`) |
72 | | -- Assuming JBrowse Web is being served on port 3000, navigate in your web |
73 | | - browser to |
74 | | - http://localhost:3000/?config=http://localhost:9000/jbrowse_config.json |
75 | | -- When you make changes to your plugin, it will automatically be re-built. |
76 | | - You can then refresh JBrowse Web to see the changes. |
77 | | - |
78 | | -### Testing |
79 | | - |
80 | | -To test your plugin, there are several commands available: |
81 | | - |
82 | | -#### `yarn browse` or `npm run browse` |
83 | | - |
84 | | -Launches your local JBrowse 2 build that is used for integration testing, with your |
85 | | -plugin already included in the configuration. Your plugin must also be running |
86 | | -(`yarn start` or `npm run start`). |
87 | | - |
88 | | -#### `yarn test` or `npm test` |
89 | | - |
90 | | -Runs any unit tests defined during plugin development. |
91 | | - |
92 | | -#### `yarn test:cy` or `npm run test:cy` |
93 | | - |
94 | | -Runs the [cypress](https://www.cypress.io/) integration tests for your plugin. |
95 | | -Both the plugin and `browse` must already be running. |
96 | | - |
97 | | -#### `yarn e2e` or `npm run e2e` |
98 | | - |
99 | | -Starts up the JBrowse 2 build as well as your plugin, and runs the [cypress](https://www.cypress.io/) |
100 | | -integration tests against them. Closes both resources after tests finish. |
101 | | - |
102 | | -#### `yarn cypress` or `npm run cypress` |
103 | | - |
104 | | -Launches the [cypress](https://www.cypress.io/) test runner, which can be very |
105 | | -useful for writing integration tests for your plugin. Both the plugin and `browse` |
106 | | -must already be running. |
107 | | - |
108 | | -#### Github Action |
109 | | - |
110 | | -This template includes a [Github action](https://github.com/features/actions) that |
111 | | -runs your integration tests when you push new changes to your repository. |
112 | | - |
113 | | -### Publishing |
114 | | - |
115 | | -Once you have developed your plugin, you can publish it to NPM. Remember to |
116 | | -remove `"private": true` from `package.json` before doing so. |
117 | | - |
118 | | -If you are using `@jbrowse/react-linear-genome-view`, you can install the plugin |
119 | | -from NPM and use it there. If you are using JBrowse Web, after the plugin is |
120 | | -published to NPM, you can use [unpkg](https://unpkg.com/) to host plugin bundle. |
121 | | -A JBrowse Web config using this plugin would look like this: |
122 | | - |
123 | | -```json |
124 | | -{ |
125 | | - "plugins": [ |
126 | | - { |
127 | | - "name": "MyProject", |
128 | | - "url": "https://unpkg.com/jbrowse-plugin-my-project/dist/jbrowse-plugin-my-project.umd.production.min.js" |
129 | | - } |
130 | | - ] |
131 | | -} |
132 | | -``` |
133 | | - |
134 | | -You can also use a specific version in unpkg, such as |
135 | | -`https://unpkg.com/[email protected]/dist/jbrowse-plugin-my-project.umd.production.min.js` |
136 | | - |
137 | | -### TypeScript vs. JavaScript |
138 | | - |
139 | | -This template is set up in such a way that you can use both TypeScript and |
140 | | -JavaScript for development. If using only JavaScript, you can change |
141 | | -`src/index.ts` to `src/index.js`. If using only TypeScript, you can remove |
142 | | -`"allowJs": true` from `tsconfig.json` and `"@babel/preset-react"` from |
143 | | -`.babelrc` (and from "devDependencies" in `package.json`). |
| 17 | +We welcome an contributions or PRs to this repo. Developer information for this |
| 18 | +codebase can be found [here](https://github.com/elliothershberg/jbrowse-plugin-quantseq/CONTRIBUTING.md) |
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