Unzip JBrowse-1.12.3

README.md

@@ -17,8 +17,9 @@ time than the built release zipfiles.  Also, since the master branch code is ''i
 Make sure you have a web server installed on your development machine.  Any web server will do.
 
     cd /my/dev/webserver/root;
-    git clone --recursive git@github.com:YOURACCOUNT/jbrowse.git
+    git clone https://github.com/GMOD/jbrowse jbrowse 
     cd jbrowse
+    bower --allow-root -f install
     ./setup.sh
     # and now point your browser to
     #   http://localhost/jbrowse/index.html?data=sample_data/json/volvox
@@ -27,11 +28,12 @@ Make sure you have a web server installed on your development machine.  Any web
 
 Then you can simply edit files and your changes will be available in the browser (i.e. no build step is required)
 
-You can also optionally run build steps to create the minimized codebase
+You can also optionally run build steps to create the minimized codebase. Extra dependencies Text::Markdown and DateTime are required to run the build step.
 
-    make -f build/Makefile release
+    make -f build/Makefile release-notest
+    make -f build/Makefile release # alternate build with full test suite
 
-To build the Electron app, run the following
+To build the Electron app (JBrowse desktop app), run the following
 
     npm install -g electron-packager
     make -f build/Makefile release-electron-all
@@ -68,8 +70,6 @@ eggs for `selenium` and `nose` installed.  Run the tests with:
 
 # Cutting a JBrowse release
 
-0. Create a directory and clone the repo: git clone --recursive https://github.com/GMOD/jbrowse.git  Then for 1.12.1, git checkout tags/1.12.1-release (because it lives in a branch that is not master) 
-
 1. Edit the JBrowse `package.json` file and change 'version' to the version you are releasing.  *Don't commit this change to the repository, it should stay as `dev` in git so that it shows up in analytics as a development version.*
 
 2. Build the release packages: `make -f build/Makefile release`.  The files produced during the build should not be committed to the repository either. There is also `make -f build/Makefile release-notest` for releases that don't need perl tests to be run. NOTE: you may need to use the command `ulimit -n 1000` to avoid "spawn EMFILE" build errors.

bin/maker2jbrowse

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use strict;
 use warnings;

bin/prepare-refseqs.pl

@@ -20,7 +20,9 @@ =head1 USAGE
    # OR:
        prepare-refseqs.pl --fasta <file1> --fasta <file2>  [options]
    # OR:
-       prepare-refseqs.pl --indexed_fasta <file1>  [options]
+       prepare-refseqs.pl --indexed_fasta <file>  [options]
+   # OR:
+       prepare-refseqs.pl --twobit <file>  [options]
    # OR:
        prepare-refseqs.pl --conf <JBrowse config file>  [options]
    # OR:

bower.json

@@ -0,0 +1,19 @@
+{
+  "name": "jbrowse",
+  "version": "1.12.2-SNAPSHOT",
+  "dependencies": {
+    "dojo":         "1.9.8",
+    "dojox":        "1.9.8",
+    "dijit":        "1.9.8",
+    "util":         "dojo/util#1.9.8",
+    "put-selector": "0.3.6",
+    "dgrid":        "0.3.17",
+    "xstyle":       "0.3.2",
+    "jDataView":    "rbuels/jDataView",
+    "jszlib":       "rbuels/jszlib",
+    "FileSaver":    "dkasenberg/FileSaver.js",
+    "json-schema":  "kriszyp/json-schema#0.2.1",
+    "lazyload":     "rbuels/lazyload#amd",
+    "dbind":        "rbuels/dbind"
+  }
+}

browser/main.js

@@ -1,26 +1,44 @@
-var app = require('app');
-var BrowserWindow = require('browser-window');
-var Menu = require('menu');
+const electron = require('electron');
+const app = electron.app;
+const BrowserWindow = electron.BrowserWindow;
+const Menu = electron.Menu;
 
 var menu = require('./menu');
 
-var mainWindow;
+// Keep a global reference of the window object, if you don't, the window will
+// be closed automatically when the JavaScript object is garbage collected.
+let mainWindow;
 
-app.on('window-all-closed', function () {
-	app.quit();
+
+
+// This method will be called when Electron has finished
+// initialization and is ready to create browser windows.
+// Some APIs can only be used after this event occurs.
+app.on('ready', function() {
+    // Create the browser window.
+    mainWindow = new BrowserWindow({
+        center: true,
+        title: 'JBrowseDesktop',
+        width: 1024,
+        height: 768
+    });
+
+    // and load the index.html of the app.
+    mainWindow.loadURL('file://' + require('path').resolve(__dirname, '..', 'index.html'));
+    // Emitted when the window is closed.
+    Menu.setApplicationMenu(Menu.buildFromTemplate(menu));
+
+    mainWindow.on('closed', function () {
+        // Dereference the window object, usually you would store windows
+        // in an array if your app supports multi windows, this is the time
+        // when you should delete the corresponding element.
+        mainWindow = null;
+    });
 });
 
-app.on('ready', function () {
-	mainWindow = new BrowserWindow({
-		center: true,
-		title: 'JBrowseDesktop',
-		width: 1024,
-		height: 768
-	});
-
-	Menu.setApplicationMenu(Menu.buildFromTemplate(menu));
-	mainWindow.loadURL('file://' + require('path').resolve(__dirname, '..', 'index.html'));
-	mainWindow.on('closed', function () {
-		mainWindow = null;
-	});
+// Quit when all windows are closed.
+app.on('window-all-closed', function () {
+    app.quit();
 });
+
+

browser/menu.js

@@ -1,5 +1,5 @@
-var app = require('app');
-var BrowserWindow = require('browser-window');
+var app = require('electron').app;
+var BrowserWindow = require('electron').BrowserWindow;
 
 var menu = module.exports = [];
 var isDarwin = process.platform === 'darwin';
@@ -27,7 +27,7 @@ menu.push(
                 label: '&Reload',
                 accelerator: 'CmdOrCtrl+R',
                 click: function () {
-                    BrowserWindow.getFocusedWindow().reloadIgnoringCache();
+                    BrowserWindow.getFocusedWindow().webContents.reloadIgnoringCache();
                 }
             },
             {

compat_121.html

@@ -23,6 +23,11 @@
                                            include: [
                                              { url: dataRoot + "/trackInfo.js", version: 0 }
                                            ],
+                                           plugins: [
+                                                   "NeatHTMLFeatures",
+                                                   "NeatCanvasFeatures",
+                                                   "HideTrackLabels"
+                                           ],
                                            nameUrl: dataRoot + "/names/root.json",
                                            defaultTracks: "DNA,gene,mRNA,noncodingRNA",
                                            queryParams: queryParams,

css/genome.css

@@ -5,6 +5,7 @@
 
 @import url("main.css");
 @import url("sequence.css");
+@import url("protein.css");
 @import url("menubar.css");
 @import url("toolbar.css");
 @import url("icons.css");

css/main.css

@@ -55,6 +55,20 @@ html, body {
     border-right-width: 1px;
 }
 
+.track .global_highlight_mod {
+    position: absolute;
+    background: rgba( 255, 255, 0, 0.7 );
+    box-sizing: border-box;
+
+    border: 1px solid black;
+    border-width: 0;
+}
+.track .global_highlight_mod.left {
+    border-left-width: 1px;
+}
+.track .global_highlight_mod.right {
+    border-right-width: 1px;
+}
 
 .tundra input {
     outline: none;
@@ -81,6 +95,16 @@ fieldset > legend {
     font-size: 14px;
 }
 
+.verticaltext {
+    transform: rotate(-90deg);
+    position: absolute;
+    border: 1px solid black;
+}
+.horizontaltext {
+    position: absolute;
+    border: 1px solid black;
+}
+
 /* styles for the autocomplete menu */
 .dijitComboBoxMenu .locString, .dijitComboBoxMenu .multipleLocations {
     margin-left: 1em;
@@ -1053,3 +1077,17 @@ table.baseQuality td {
     display: block;
     text-align: center;
 }
+
+.about-dialog .loaded-plugins {
+    text-align: left;
+}
+
+.about-dialog .loaded-plugins li {
+    margin: 0em;
+}
+
+.about-dialog .plugins-list {
+    max-height: 100px;
+    overflow: auto;
+}
+