Add docs for sequence track, variant track, launching synteny from dotplot, and add UCSC plugin to demo

CONTRIBUTING.md

@@ -98,3 +98,116 @@ release and click "Edit," then add a description to the release. Usually you
 can copy the content of the blog post that was generated (it will be named
 something like `website/blog/${DATE}-${RELEASE_TAG}-release.md`), removing the
 "Downloads" section. Finally, click "Publish release."
+
+## Monorepo code organization
+
+JBrowse 2 code is organized as a monorepo using [lerna](https://lerna.js.org/)
+and [yarn workspaces](https://classic.yarnpkg.com/en/docs/workspaces/). Using a
+monorepo means that instead of separate GitHub repositories for each piece of
+JBrowse, they are all in a single place and can share code easily. In the top
+level of the repository there are two directories, `packages/` and `products/`
+that each contain multiple packages.
+
+Each "package" is an npm-style (i.e. contains `package.json`) package. The
+packages in `packages/` are core code, development tools, etc. The packages in
+`plugins/` are JBrowse plugins. Most of JBrowse is written as plugins, so that
+is where most of the code is. The packages in `products/` are user-facing
+products, such as JBrowse Web, JBrowse Desktop, JBrowse CLI, etc.
+
+### Monorepo packages
+
+The following is a summary of some of the individual packages in the monorepo.
+It's not a comprehensive list, but will hopefully help familiarize you with how
+the code is organized.
+
+#### products/jbrowse-web
+
+This is the full JBrowse Web app. It is built using
+[create-react-app](https://create-react-app.dev/).
+
+It includes many other packages as core plugins, can load other plugins at
+runtime, and more.
+
+It also currently holds the "integration tests" that we use for our code in
+`products/jbrowse-web/src/tests`.
+
+#### products/jbrowse-desktop
+
+JBrowse Desktop is our essentially the same as JBrowse Web, but packaged with
+[electron](https://www.electronjs.org/) into a desktop app. This gives it the
+ability to easily load and save tracks based on files on your local filesystem.
+It also has save sessions locally, and works offline.
+
+#### products/website
+
+This provides the docusaurus website with docs, blog, and pdf documentation
+
+#### plugins/alignments
+
+This package provides the "alignments" related features including
+
+- BamAdapter - our BAM parser that wraps @gmod/bam NPM module
+- CramAdapter - our CRAM parser that wraps the @gmod/cram NPM module
+- PileupTrack type - draws alignments as boxes in a "pileup" style view
+- SNPCoverageTrack - draws calculated coverage with mismatches drawn over the coverage
+- AlignmentsTrack - a "supertrack" which contains a PileupTrack and
+  SNPCoverageTrack "subtracks"
+- AlignmentsFeatureWidget for alignments features
+
+#### plugins/variants/
+
+Provides variant features including
+
+- VCF tabix parser
+- VariantFeatureWidget
+- VariantTrack that is basically just a normal track, but has logic to popup
+  the VariantFeatureWidget on feature click
+
+#### plugins/hic
+
+This provides a HicAdapter based on the .hic file format
+([ref](https://github.com/aidenlab/juicer/wiki/Data#hic-files))
+
+Also a track type and renderer to visualize these
+
+#### plugins/bed
+
+Provides two bed related data adapters
+
+- BigBedAdapter
+- BedTabixAdapter
+
+These can be used with the SvgFeatureRenderer
+
+#### plugins/wiggle
+
+Provides wiggle track types with different types of rendering formats including
+
+- XYPlotRenderer
+- LinePlotRenderer
+- DensityRenderer
+
+The WiggleTrack type can swap out these different rendering types, and
+calculates stats such as max and min score over a region before the region is
+rendered
+
+#### plugins/svg
+
+This is the main gene glyphs, which are rendered using SVG
+
+General usage of this involves referencing the SvgFeatureRenderer
+
+#### plugins/spreadsheet-view
+
+This provides a spreadsheet-in-the-browser that can be used as a data backend
+to power other views
+
+#### plugins/circular-view
+
+This provides our 'Circos-style' whole-genome overview of data, especially
+genomic translocations
+
+#### plugins/sv-inspector
+
+This is a "superview" type that contains a circular and spreadsheet view as
+child views

test_data/config_demo.json

@@ -8,6 +8,10 @@
     {
       "name": "GDC",
       "url": "https://ghcdn.rawgit.org/GMOD/jbrowse-plugin-gdc/master/dist/plugin.js"
+    },
+    {
+      "name": "UCSC",
+      "url": "https://ghcdn.rawgit.org/cmdcolin/jbrowse-plugin-ucsc-api/master/dist/plugin.js"
     }
   ],
   "assemblies": [
@@ -205,6 +209,28 @@
         "type": "MyGeneV3Adapter"
       }
     },
+    {
+      "type": "FeatureTrack",
+      "trackId": "genehancer_ucsc_hg38",
+      "name": "UCSC GeneHancer",
+      "category": ["Annotation"],
+      "assemblyNames": ["hg38"],
+      "adapter": {
+        "type": "UCSCAdapter",
+        "track": "geneHancerInteractionsDoubleElite"
+      }
+    },
+    {
+      "type": "FeatureTrack",
+      "trackId": "genehancer_ucsc_hg19",
+      "name": "UCSC GeneHancer",
+      "category": ["Annotation"],
+      "assemblyNames": ["hg19"],
+      "adapter": {
+        "type": "UCSCAdapter",
+        "track": "geneHancerInteractionsDoubleElite"
+      }
+    },
     {
       "type": "GDCTrack",
       "trackId": "gdc_plugin_track",

website/blog/2020-10-22-jbrowse-web-0.0.1-beta.27-release.md

@@ -1,5 +1,5 @@
 ---
-title: jbrowse-web 0.0.1-beta.27
+title: v0.0.1-beta.27 Release
 date: 2020-10-22
 tags: ['release', 'jbrowse 2']
 ---

website/blog/2020-10-31-jbrowse-web-0.0.1-beta.28-release.md

@@ -1,5 +1,5 @@
 ---
-title: jbrowse-web 0.0.1-beta.28
+title: v0.0.1-beta.28 Release
 date: 2020-10-31
 tags: ['release', 'jbrowse 2']
 ---

website/blog/2020-11-05-jbrowse-web-1.0.0-release.md

@@ -1,5 +1,5 @@
 ---
-title: jbrowse-web 1.0.0
+title: v1.0.0 Release
 date: 2020-11-05
 tags: ['release', 'jbrowse 2']
 ---

website/docs/developer_guide.md

@@ -4,10 +4,9 @@ title: Developer guide
 toplevel: true
 ---
 
-In this Developer Guide, will introduce the JBrowse 2 ecosystem from the
-developer's point of view. We'll examine the core concepts of how code is
-packaged and structured, and then go over how to create new plugins and
-pluggable elements.
+In this guide, will introduce the JBrowse 2 ecosystem from the developer's
+point of view. We'll examine the core concepts of how code is packaged and
+structured, and then go over how to create new plugins and pluggable elements.
 
 ## Introduction and overview
 
@@ -19,7 +18,6 @@ The JBrowse 2 ecosystem has two main type of top-level artifacts that are
 published on their own: products and plugins.
 
 ![](./img/products_and_plugins.png)
-
 Architecture diagram of JBrowse 2, showing how plugins encapsulate views (e.g.
 LinearGenomeView, DotplotView etc.), tracks (AlignmentsTrack, VariantTrack,
 etc.), data adapters (BamAdapter, VcfTabixAdapter, etc.) and other logic like
@@ -399,7 +397,7 @@ Add a menu item to a sub-menu
 | menuPath | Path to the sub-menu to add to, starting with the top-level menu (e.g. `['File', 'Insert']`). |
 | menuItem | Menu item to append.                                                                          |
 
-##### Return Value
+##### Return value
 
 The new length of the sub-menu
 
@@ -415,7 +413,7 @@ Insert a menu item into a sub-menu
 | menuItem | Menu item to insert.                                                                                                                             |
 | position | Position to insert menu item. If negative, counts from the end, e.g. `insertMenu('My Menu', -1)` will insert the menu as the second-to-last one. |
 
-##### Return Value
+##### Return value
 
 The new length of the sub-menu
 
@@ -442,7 +440,7 @@ types
   }))
 ```
 
-### Adding track context menu items
+### Adding track context-menu items
 
 When you right-click in a linear track, a context menu will appear if there are
 any menu items defined for it. It's possible to add items to that menu, and you
@@ -496,120 +494,7 @@ class SomePlugin extends Plugin {
 }
 ```
 
-## Monorepo code organization
-
-JBrowse 2 code is organized as a monorepo using [lerna](https://lerna.js.org/)
-and [yarn workspaces](https://classic.yarnpkg.com/en/docs/workspaces/). Using a
-monorepo means that instead of separate GitHub repositories for each piece of
-JBrowse, they are all in a single place and can share code easily. In the top
-level of the repository there are two directories, `packages/` and `products/`
-that each contain multiple packages.
-
-Each "package" is an npm-style (i.e. contains `package.json`) package. The
-packages in `packages/` are core code, development tools, etc. The packages in
-`plugins/` are JBrowse plugins. Most of JBrowse is written as plugins, so that
-is where most of the code is. The packages in `products/` are user-facing
-products, such as JBrowse Web, JBrowse Desktop, JBrowse CLI, etc.
-
-### Monorepo packages
-
-The following is a summary of some of the individual packages in the monorepo.
-It's not a comprehensive list, but will hopefully help familiarize you with how
-the code is organized.
-
-#### products/jbrowse-web
-
-This is the full JBrowse Web app. It is built using
-[create-react-app](https://create-react-app.dev/).
-
-It includes many other packages as core plugins, can load other plugins at
-runtime, and more.
-
-It also currently holds the "integration tests" that we use for our code in
-`products/jbrowse-web/src/tests`.
-
-#### products/jbrowse-desktop
-
-JBrowse Desktop is our essentially the same as JBrowse Web, but packaged with
-[electron](https://www.electronjs.org/) into a desktop app. This gives it the
-ability to easily load and save tracks based on files on your local filesystem.
-It also has save sessions locally, and works offline.
-
-#### products/website
-
-This provides the docusaurus website with docs, blog, and pdf documentation
-
-#### plugins/alignments
-
-This package provides the "alignments" related features including
-
-- BamAdapter - our BAM parser that wraps @gmod/bam NPM module
-- CramAdapter - our CRAM parser that wraps the @gmod/cram NPM module
-- PileupTrack type - draws alignments as boxes in a "pileup" style view
-- SNPCoverageTrack - draws calculated coverage with mismatches drawn over the coverage
-- AlignmentsTrack - a "supertrack" which contains a PileupTrack and
-  SNPCoverageTrack "subtracks"
-- AlignmentsFeatureWidget for alignments features
-
-#### plugins/variants/
-
-Provides variant features including
-
-- VCF tabix parser
-- VariantFeatureWidget
-- VariantTrack that is basically just a normal track, but has logic to popup
-  the VariantFeatureWidget on feature click
-
-#### plugins/hic
-
-This provides a HicAdapter based on the .hic file format
-([ref](https://github.com/aidenlab/juicer/wiki/Data#hic-files))
-
-Also a track type and renderer to visualize these
-
-#### plugins/bed
-
-Provides two bed related data adapters
-
-- BigBedAdapter
-- BedTabixAdapter
-
-These can be used with the SvgFeatureRenderer
-
-#### plugins/wiggle
-
-Provides wiggle track types with different types of rendering formats including
-
-- XYPlotRenderer
-- LinePlotRenderer
-- DensityRenderer
-
-The WiggleTrack type can swap out these different rendering types, and
-calculates stats such as max and min score over a region before the region is
-rendered
-
-#### plugins/svg
-
-This is the main gene glyphs, which are rendered using SVG
-
-General usage of this involves referencing the SvgFeatureRenderer
-
-#### plugins/spreadsheet-view
-
-This provides a spreadsheet-in-the-browser that can be used as a data backend
-to power other views
-
-#### plugins/circular-view
-
-This provides our 'Circos-style' whole-genome overview of data, especially
-genomic translocations
-
-#### plugins/sv-inspector
-
-This is a "superview" type that contains a circular and spreadsheet view as
-child views
-
-### Plugin Build system
+### Plugin build system
 
 Plugins may be built as separate packages that can be distributed on NPM. In
 order to streamline development and avoid having to build every plugin before
@@ -997,15 +882,30 @@ instead of manually cleaning up resources
 
 ## Creating a new plugin
 
+We have a couple plugin examples here
+
+- https://github.com/GMOD/jbrowse-plugin-gdc - demonstrates accessing GDC
+  cancer data GraphQL API, plus a custom drawer and track type for coloring
+  variants by impact score
+- https://github.com/cmdcolin/jbrowse-plugin-biothings-api - demonstrates
+  accessing data from mygene.info, part of the "biothings API" family
+- https://github.com/cmdcolin/jbrowse-plugin-ucsc-api - demonstrates accessing
+  data from UCSC
+
+We will go over in detail some of these steps. Note that the best practices
+may be found by looking at the above plugins source code directly, and you can
+copy these plugins as a template for your own.
+
+### Intro to plugins
+
 JBrowse 2 plugins can be used to add new pluggable elements (views, tracks,
 data adapters, etc), and to modify behavior of the application by adding code
 that watches the application's state. For the full list of what kinds of
 pluggable element types plugins can add, see the [pluggable
 elements](developer_guide#pluggable-elements) page.
 
-We will go over creating an example plugin. The first thing that we have is a
-`src/index.js` which exports a default class containing the plugin registration
-code
+The first thing that we have is a `src/index.js` which exports a default class
+containing the plugin registration code
 
 src/index.js