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Updating Node Deps #1626

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Updating Node Deps #1626

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fd7ebb8
Add note to link to jbrowse 2
cmdcolin Apr 2, 2021
d12d3b1
Update README.md
cmdcolin Jun 21, 2021
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Update yarn.lock
childers Feb 3, 2022
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Update package.json
childers Feb 3, 2022
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40 changes: 21 additions & 19 deletions README.md
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@@ -1,11 +1,17 @@
[![Build status](https://travis-ci.org/GMOD/jbrowse.svg?branch=dev)](https://travis-ci.org/GMOD/jbrowse)
[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v1.4%20adopted-ff69b4.svg)](CODE_OF_CONDUCT.md)

Note: most of our current development is on JBrowse 2, see our github repo here https://github.com/gmod/jbrowse-components

We will still continue to make bug fix and maintenance releases of JBrowse 1 but most development is on JBrowse 2

Note: if you are using plugins with a dev version of JBrowse or installing from GitHub, you may need to use node <=14 (e.g. node >=15 may fail) due to node-sass not compiling on newer node versions easily. See https://github.com/GMOD/jbrowse/pull/1607 for details


# Installing JBrowse

To install jbrowse, visit http://jbrowse.org/blog and download the latest JBrowse zip file. See instructions at http://jbrowse.org/docs/installation.html for a tutorial on setting up a sample instance.


# Install JBrowse from GitHub (for developers)

To install from GitHub, you can simply clone the repo and run the setup.sh script
Expand All @@ -14,26 +20,26 @@ To install from GitHub, you can simply clone the repo and run the setup.sh scrip
cd jbrowse
./setup.sh




## Develop JBrowse or JBrowse plugins

To obtain a jbrowse development environment, e.g. for jbrowse source code editing or plugin development (or just running jbrowse from the github repo)


git clone https://github.com/GMOD/jbrowse
cd jbrowse
./setup.sh # not strictly necessary if you don't need to sample data

If you are going to edit the jbrowse source code, then also run

yarn watch

And keep `yarn watch` running in the background as you create changes to your code.

To start a temporary dev server, can also run

yarn start

And keep this running in the background, this will launch a webserver running jbrowse on port 8082.

Alternatively, you can put this jbrowse folder in your webserver (e.g. /var/www/html/) directory. The key is, if you are modifying jbrowse or plugin source code, to run `yarn watch` in the background, so that webpack incorporates your changes in either the main codebase (src/JBrowse folder) or any plugins (plugins/YourPlugin).
Expand All @@ -46,20 +52,17 @@ In order to make downloads faster you can set a mirror for the npm registry
npm config set puppeteer_download_host=http://cnpmjs.org/mirrors
export ELECTRON_MIRROR="http://cnpmjs.org/mirrors/electron/"


## Notes on setting up a JBrowse server

* If you don't have a webserver such as apache or nginx, you can run `npm run start` and open http://localhost:8082/index.html?data=sample_data/json/volvox to see the code running from a small express.js server.

* You can alternatively just move the jbrowse folder into a nginx or apache root directory e.g. /var/www/html and then navigate to http://localhost/jbrowse
- If you don't have a webserver such as apache or nginx, you can run `npm run start` and open http://localhost:8082/index.html?data=sample_data/json/volvox to see the code running from a small express.js server.

- You can alternatively just move the jbrowse folder into a nginx or apache root directory e.g. /var/www/html and then navigate to http://localhost/jbrowse

_Note: you should avoid using sudo tasks like ./setup.sh and instead use chown/chmod on folders to your own user as necessary._

*Note: you should avoid using sudo tasks like ./setup.sh and instead use chown/chmod on folders to your own user as necessary.*
_Also note: After editing a file, you must re-run the webpack build with `npm run build` or you can keep webpack running in "watch" mode by running `npm run watch`._

*Also note: After editing a file, you must re-run the webpack build with `npm run build` or you can keep webpack running in "watch" mode by running `npm run watch`.*

*Also also note: by default `git clone` will clone the master branch which contains the latest stable release. The latest development branch is called dev. Run `git checkout dev` after clone to retrieve this*
_Also also note: by default `git clone` will clone the master branch which contains the latest stable release. The latest development branch is called dev. Run `git checkout dev` after clone to retrieve this_

# Installing as an npm module

Expand Down Expand Up @@ -88,14 +91,14 @@ The Travis-CI suite runs Perl, JavaScript, and Selenium automated tests. To run
pip install selenium nose
MOZ_HEADLESS=1 SELENIUM_BROWSER=firefox JBROWSE_URL='http://localhost/jbrowse/index.html' nosetests

Supported browsers for SELENIUM_BROWSER are 'firefox', 'chrome', 'phantom', and 'travis_saucelabs'. The Sauce Labs + Travis
Supported browsers for SELENIUM_BROWSER are 'firefox', 'chrome', 'phantom', and 'travis_saucelabs'. The Sauce Labs + Travis
one will only work in a properly configured Travis CI build environment.

# Manual testing

<img style="display: block; margin: 1em auto" src="img/browserstack-logo-600x315.png" width="200" alt="Browserstack"/>

JBrowse has a free open source account on [Browserstack](http://browserstack.com/) for manual testing. Contact @rbuels for access.
JBrowse has a free open source account on [Browserstack](http://browserstack.com/) for manual testing. Contact @rbuels for access.

# Generating Packaged Builds

Expand All @@ -113,13 +116,12 @@ To run the Electron app in debug mode run the following
npm install -g electron
electron browser/main.js


# Making a JBrowse release

NOTE: Beginning in 1.12.4,

1. Run `build/release.sh $newReleaseVersion $nextReleaseVersion-alpha.0 notes.txt`, where notes.txt is any additional information to add to a blogpost. Then check its work, and then run the `git push` command it suggests to you. This makes a tag in the repository for the release, named, e.g. `1.6.3-release`. This should cause Travis CI
to create a release on GitHub under https://github.com/GMOD/jbrowse/releases
1. Run `build/release.sh $newReleaseVersion $nextReleaseVersion-alpha.0 notes.txt`, where notes.txt is any additional information to add to a blogpost. Then check its work, and then run the `git push` command it suggests to you. This makes a tag in the repository for the release, named, e.g. `1.6.3-release`. This should cause Travis CI
to create a release on GitHub under https://github.com/GMOD/jbrowse/releases

1. Test that the page loads in IE11 on BrowserStack

Expand Down
27 changes: 15 additions & 12 deletions package.json
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Expand Up @@ -34,12 +34,15 @@
"dependencies": {
"express": "^4.15.4",
"fs-extra": "^4.0.1",
"node-fetch": "^2.2.0",
"ini": "^1.3.8",
"lodash": "^4.17.21",
"node-fetch": "^3.2.0",
"node-getopt": "^0.2.3",
"normalize-wheel": "^1.0.1",
"object-hash": "^1.3.1",
"optimist": "^0.6.1",
"shelljs": "^0.7.8"
"shelljs": "^0.8.5",
"y18n": "^5.0.8"
},
"devDependencies": {
"@gmod/bam": "^1.1.6",
Expand All @@ -51,7 +54,7 @@
"@gmod/twobit": "^1.1.2",
"@gmod/vcf": "^2.0.2",
"ajv": "^6.2.1",
"ava": "^0.25.0",
"ava": "^3.15.0",
"babel-core": "^6.26.0",
"babel-eslint": "^8.2.2",
"babel-loader": "^7.1.4",
Expand All @@ -60,38 +63,38 @@
"babel-polyfill": "^6.26.0",
"babel-preset-es2015-without-strict": "^0.0.4",
"clean-webpack-plugin": "^0.1.18",
"copy-webpack-plugin": "^4.6.0",
"copy-webpack-plugin": "^5.1.2",
"css-loader": "^2.0.0",
"dgrid": "^1.1.0",
"dijit": "^1.14.2",
"dojo": "^1.14.2",
"dojo": "^1.16.2",
"dojo-dstore": "^1.1.1",
"dojo-util": "^1.14.2",
"dojo-webpack-plugin": "^2.8.5",
"dojox": "^1.14.2",
"electron": "^3.0.12",
"electron-packager": "^12.0.1",
"electron": "^16.0.8",
"electron-packager": "^14.2.1",
"eslint": "^4.19.1",
"eslint-config-airbnb-base": "^12.1.0",
"eslint-plugin-import": "^2.10.0",
"filesaver.js": "^0.2.0",
"http-range-fetcher": "^1.2.1",
"http-range-fetcher": "^1.2.5",
"imports-loader": "^0.8.0",
"jasmine-node": "^3.0.0",
"node-sass": "^4.12.0",
"node-sass": "^7.0.1",
"puppeteer": "^1.0.0",
"quick-lru": "^2.0.0",
"regexp-replace-loader": "^1.0.1",
"sass-loader": "^6.0.7",
"snake-case": "^2.1.0",
"spectron": "^5.0.0",
"spectron": "^15.0.0",
"style-loader": "^0.20.2",
"tenacious-fetch": "^2.1.0",
"tmp": "^0.0.33",
"uglifyjs-webpack-plugin": "^1.2.2",
"uglifyjs-webpack-plugin": "^2.2.0",
"url-loader": "^1.0.0",
"util-deprecate": "^1.0.2",
"webpack": "^4.26.1",
"webpack": "^4.9.1",
"webpack-cli": "^3.1.2",
"whatwg-fetch": "^2.0.4",
"yarn": "^1.16.0"
Expand Down
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