Add some docs for configuring defaultSession

website/docs/config_guides/default_session.md

@@ -0,0 +1,113 @@
+---
+title: Default session
+id: default_session
+---
+
+In JBrowse, a session refers to the particular state of the application e.g. the
+views that are open, the tracks that are open, etc.
+
+You can configure a "default session" in the config.json that can be used as the
+default application state that is loaded for all your users.
+
+The session is a representation of the 'internal state' of the app, so it can be
+hard to programmatically write, but you can manually use the app, get to a state
+you want it to be in, and then select "File->Export session". This will give you
+a session.json file, and then you can copy the "session" from this file into the
+"defaultSession" in your config.json
+
+Example session (reduced for example purposes)
+
+```json
+{
+  "session": {
+    "id": "eXr4hv4VX",
+    "name": "Session",
+    "views": [
+      {
+        "id": "eXr4hv4VX-view",
+        "type": "LinearGenomeView",
+        "offsetPx": 14500,
+        "bpPerPx": 1.7,
+        "displayedRegions": [
+          {
+            "refName": "ctgA",
+            "start": 0,
+            "end": 50001,
+            "reversed": false,
+            "assemblyName": "volvox"
+          }
+        ]
+      }
+    ]
+  }
+}
+```
+
+Then copy the above into your config.json in the "defaultSession", for example:
+
+```json
+{
+  "assemblies": [
+    {
+      "name": "volvox",
+      "sequence": {
+        "type": "ReferenceSequenceTrack",
+        "trackId": "volvox_refseq",
+        "adapter": {
+          "type": "TwoBitAdapter",
+          "twoBitLocation": {
+            "uri": "volvox.2bit"
+          }
+        }
+      }
+    }
+  ],
+  "defaultSession": {
+    "id": "eXr4hv4VX",
+    "name": "Session",
+    "views": [
+      {
+        "id": "eXr4hv4VX-view",
+        "type": "LinearGenomeView",
+        "offsetPx": 14500,
+        "bpPerPx": 1.7,
+        "displayedRegions": [
+          {
+            "refName": "ctgA",
+            "start": 0,
+            "end": 50001,
+            "reversed": false,
+            "assemblyName": "volvox"
+          }
+        ]
+      }
+    ]
+  },
+  "tracks": [
+    {
+      "type": "VariantTrack",
+      "trackId": "variants",
+      "name": "variants",
+      "assemblyNames": ["volvox"],
+      "adapter": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "volvox.dup.vcf.gz"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.dup.vcf.gz.tbi"
+          }
+        }
+      }
+    }
+  ]
+}
+```
+
+:::info
+
+Note: if you want to programmatically configure sessions using the URL, see
+https://jbrowse.org/jb2/docs/urlparams/
+
+:::

website/docs/config_guides/intro.md

@@ -30,10 +30,16 @@ config.json) and is structured as follows
 
 The most important thing to configure are your assemblies and your tracks.
 
-:::info Note On jbrowse desktop, a "session" refers to a config.json with a
-.jbrowse file extension :::
+:::info
 
-:::info Note On embedded e.g. with @jbrowse/react-linaer-genome-view, it does
+Note: On jbrowse desktop, a "session" refers to a config.json with a .jbrowse
+file extension
+
+:::
+
+:::info
+
+Note: with embedded components e.g. @jbrowse/react-linear-genome-view, it does
 not accept a config file but rather an object at runtime with the config loaded.
 
 To fetch a config.json object on the fly in @jbrowse/react-linear-genome-view,