Suggested Improvements as a Non-JS Developer

[laceysanderson]

This issue is a placeholder for my own feedback as I walk through this template to make my first jbrowse plugin. I come from the PHP/Tripal world so have a very beginner perspective.

It would be very helpful to include a dockerfile to help people get started! Here's my current stab at this in my plugin: https://github.com/tripal/Tripal-JBrowse-InternetAccountPlugin/blob/main/Dockerfile

When filling out the repository prompting,

• it would be good to mention the format you want the licence in. It should indicate SPDX and provide a site to lookup other options.
• when asking if we want it private or not, it should mention this indicates whether it shows up on NPM and that it does not impact whether it's on the JBrowse plugin listing.

Note: when running yarn you currently see the following warnings:

warning " > @jbrowse/development-tools@2.1.1" has unmet peer dependency "regenerator-runtime@^0.13.0".
warning " > @jbrowse/development-tools@2.1.1" has incorrect peer dependency "rollup@^2.0.0".
warning " > @jbrowse/development-tools@2.1.1" has unmet peer dependency "tslib@^2.0.0".
warning " > @jbrowse/development-tools@2.1.1" has incorrect peer dependency "typescript@^4.0.0".
warning "@jbrowse/development-tools > @rollup/plugin-babel@5.3.1" has incorrect peer dependency "rollup@^1.20.0||^2.0.0".
warning "@jbrowse/development-tools > @rollup/plugin-commonjs@19.0.2" has incorrect peer dependency "rollup@^2.38.3".
warning "@jbrowse/development-tools > @rollup/plugin-json@4.1.0" has incorrect peer dependency "rollup@^1.20.0 || ^2.0.0".
warning "@jbrowse/development-tools > @rollup/plugin-node-resolve@13.3.0" has incorrect peer dependency "rollup@^2.42.0".
warning "@jbrowse/development-tools > @rollup/plugin-typescript@8.5.0" has incorrect peer dependency "rollup@^2.14.0".
warning "@jbrowse/development-tools > rollup-plugin-external-globals@0.6.1" has incorrect peer dependency "rollup@^2.25.0".
warning "@jbrowse/development-tools > rollup-plugin-terser@7.0.2" has incorrect peer dependency "rollup@^2.0.0".
warning "@jbrowse/development-tools > @rollup/plugin-babel > @rollup/pluginutils@3.1.0" has incorrect peer dependency "rollup@^1.20.0||^2.0.0".

As a non-react developer it's not clear that I need to run build after setup since setup also mentions that it adds a build of JBrowse 2.

When I try to serve the site, I get an error and it opens on port 9000.

yarn start
yarn run v1.22.22
$ npm-run-all --sequential clean --parallel start:*
$ rimraf dist
$ cross-env JB_NPM=false NODE_ENV=development rollup --config --watch --bundleConfigAsCjs
$ serve --cors --listen $npm_package_config_port .
(node:313) [DEP0040] DeprecationWarning: The `punycode` module is deprecated. Please use a userland alternative instead.
(Use `node --trace-deprecation ...` to show where the warning was created)
 ERROR  Cannot copy server address to clipboard: Couldn't find the `xsel` binary and fallback didn't work. On Debian/Ubuntu you can install xsel with: sudo apt install xsel.

   ┌────────────────────────────────────────┐
   │                                        │
   │   Serving!                             │
   │                                        │
   │   - Local:    http://localhost:9000    │
   │   - Network:  http://172.17.0.2:9000   │
   │                                        │
   └────────────────────────────────────────┘

Seeing the red deprecation made me think something was really wrong but apparently it's fine.

It wasn't clear to me that I needed to run both yarn start and yarn browse and that I should see my jbrowse in http://localhost:8999.

I am working on doing everything in a dockerfile and having both commands is problematic in that case. Instead I added a new yarn startbrowse command that could be my docker container entrypoint. You can see that here: https://github.com/tripal/Tripal-JBrowse-InternetAccountPlugin/blob/main/package.json#L39