fixing image references

Author: MahdiSayadSadr

Juicebox.wiki/Bookmarks.md

@@ -2,25 +2,25 @@
 ##Loading Location##
 You can use the Bookmarks menu to save and restore location and resolution data. Select *Bookmarks* and choose *Save current location*. A pop up window will appear and ask for a name to associate with the position. Enter a description for the new bookmark. Choosing *Restore saved location* will then navigate immediately to the location and resolution in the current map. The location can also be opened in another map. Saved location are kept in registry and can be used after restarting Juicebox.
 
-<img width=275 height=119 class="centered" src="images/navigation/image032.png" alt=""/>
+<img width=275 height=119 class="centered" src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/navigation/image032.png" alt=""/>
 
 ##Save State##
 
 Under the Bookmarks menu, there is an option to Save current state which allows you to save your current workspace, or state, in Juicebox. A *state* includes the loaded HiC map, matrix type, location, normalization, loaded tracks, etc.
 
-<img width=275 height=119 class="centered" src="images/state/1.png" alt="Pic of bookmark menu/save current state option"/>
+<img width=275 height=119 class="centered" src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/state/1.png" alt="Pic of bookmark menu/save current state option"/>
 
 You have the option to reload these states by going to the Restore previous states option under the Bookmarks tab, which will be filled with a list of your saved states.
 
-<img width=275 height=119 class="centered" src="images/state/2.png" alt="pic of restore previous states"/>
+<img width=275 height=119 class="centered" src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/state/2.png" alt="pic of restore previous states"/>
 
 Upon clicking the Save current state option, you will be prompted to select a name for your current state. If a state with that name already exists, you have the option to rename it or to overwrite it.
 
-<img width=275 height=119 class="centered" src="images/state/3.png" alt="pic of yes/no pane for overwrite"/>
+<img width=275 height=119 class="centered" src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/state/3.png" alt="pic of yes/no pane for overwrite"/>
 
 Under the Bookmarks tab, there are options Export Saved States and Import States From File which allow you to share your “saved states” with other Juicebox users.
 
-<img width=275 height=119 class="centered" src="images/state/4.png" alt="pic of import/export option"/>
+<img width=275 height=119 class="centered" src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/state/4.png" alt="pic of import/export option"/>
 
 When exporting a file, you can choose what to name your file and where to save it. You can share your states with others through E-mail, Dropbox, etc.
 

Juicebox.wiki/Download.md

@@ -6,60 +6,61 @@ Newer jar releases are posted under [Github Releases](https://github.com/aidenla
 
 *Due to active development, bugs may be encountered. Please email us or create a github issue for these bugs and we will fix them ASAP.*
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/Juicebox/Juicebox_1.11.08.exe"><img src="images/winlogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/Juicebox/Juicebox_1.11.08.exe">Juicebox with Assembly Tools for Windows (Signed EXE)</a>
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/Juicebox/Juicebox_1.11.08.dmg"><img src="images/maclogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/Juicebox/Juicebox_1.11.08.dmg">Juicebox with Assembly Tools for Mac (Signed DMG)</a>
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/Juicebox/Juicebox_1.11.08.exe"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/winlogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/Juicebox/Juicebox_1.11.08.exe">Juicebox with Assembly Tools for Windows (Signed EXE)</a>
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/Juicebox/Juicebox_1.11.08.jar"><img src="images/javalogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/Juicebox/Juicebox_1.11.08.jar">Juicebox with Assembly Tools for Unix, Windows, etc. (Signed JAR)</a>
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/Juicebox/Juicebox_1.11.08.dmg"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/maclogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/Juicebox/Juicebox_1.11.08.dmg">Juicebox with Assembly Tools for Mac (Signed DMG)</a>
+
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/Juicebox/Juicebox_1.11.08.jar"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/javalogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/Juicebox/Juicebox_1.11.08.jar">Juicebox with Assembly Tools for Unix, Windows, etc. (Signed JAR)</a>
 
 Juicebox requires Java: [download Java here](https://java.com/en/download/)
 
 **On Windows, be sure to download 64-bit Java**: [direct link here](http://javadl.oracle.com/webapps/download/AutoDL?BundleId=218833_e9e7ea248e2c4826b92b3f075a80e441)
 
 ##  Version (1.9.8)
 
-<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/Juicebox/Juicebox_1.9.8.exe"><img src="images/winlogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/Juicebox/Juicebox_1.9.8.exe">Juicebox with Assembly Tools for Windows (Signed EXE)</a>
+<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/Juicebox/Juicebox_1.9.8.exe"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/winlogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/Juicebox/Juicebox_1.9.8.exe">Juicebox with Assembly Tools for Windows (Signed EXE)</a>
 
-<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/Juicebox/Juicebox_1.9.8.dmg"><img src="images/maclogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/Juicebox/Juicebox_1.9.8.dmg">Juicebox with Assembly Tools for Mac (Signed DMG)</a>
+<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/Juicebox/Juicebox_1.9.8.dmg"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/maclogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/Juicebox/Juicebox_1.9.8.dmg">Juicebox with Assembly Tools for Mac (Signed DMG)</a>
 
-<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/Juicebox/Juicebox_1.9.8.jar"><img src="images/javalogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/Juicebox/Juicebox_1.9.8.jar">Juicebox with Assembly Tools for Unix, Windows, etc. (Signed JAR)</a>
+<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/Juicebox/Juicebox_1.9.8.jar"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/javalogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/Juicebox/Juicebox_1.9.8.jar">Juicebox with Assembly Tools for Unix, Windows, etc. (Signed JAR)</a>
 
 ## Version (1.8.8/1.9.0)
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox_1.8.8.exe"><img src="images/winlogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox_1.8.8.exe">Juicebox with Assembly Tools for Windows (Signed EXE)</a>
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox_1.8.8.exe"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/winlogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox_1.8.8.exe">Juicebox with Assembly Tools for Windows (Signed EXE)</a>
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox_1.9.0.dmg"><img src="images/maclogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox_1.9.0.dmg">Juicebox with Assembly Tools for Mac (Signed DMG)</a> [updated to 1.9.0 for Mac-specific font and speed issue]
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox_1.9.0.dmg"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/maclogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox_1.9.0.dmg">Juicebox with Assembly Tools for Mac (Signed DMG)</a> [updated to 1.9.0 for Mac-specific font and speed issue]
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox_1.8.8.jar"><img src="images/javalogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox_1.8.8.jar">Juicebox with Assembly Tools for Unix, Windows, etc. (Signed JAR)</a>
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox_1.8.8.jar"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/javalogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox_1.8.8.jar">Juicebox with Assembly Tools for Unix, Windows, etc. (Signed JAR)</a>
 
 ## Version 1.6.11
 
-<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/juicebox/Juicebox.1.6.11.exe"><img src="images/winlogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/juicebox/Juicebox.1.6.11.exe">Juicebox for Windows</a>
+<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/juicebox/Juicebox.1.6.11.exe"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/winlogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/juicebox/Juicebox.1.6.11.exe">Juicebox for Windows</a>
 
-<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/juicebox/Juicebox.1.6.11.dmg"><img src="images/maclogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/juicebox/Juicebox.1.6.11.dmg">Juicebox for Mac</a>
+<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/juicebox/Juicebox.1.6.11.dmg"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/maclogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/juicebox/Juicebox.1.6.11.dmg">Juicebox for Mac</a>
 
-<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/juicebox/Juicebox.1.6.11.jar"><img src="images/javalogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/juicebox/Juicebox.1.6.11.jar">Juicebox jar (Unix, Windows, etc.)</a>
+<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/juicebox/Juicebox.1.6.11.jar"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/javalogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://hicfiles.tc4ga.com.s3.amazonaws.com/public/juicebox/Juicebox.1.6.11.jar">Juicebox jar (Unix, Windows, etc.)</a>
 
 ## Version 1.6.2
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.2.exe"><img src="images/winlogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.2.exe">Juicebox for Windows</a>
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.2.exe"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/winlogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.2.exe">Juicebox for Windows</a>
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.2.dmg"><img src="images/maclogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.2.dmg">Juicebox for Mac</a>
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.2.dmg"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/maclogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.2.dmg">Juicebox for Mac</a>
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.2.jar"><img src="images/javalogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.2.jar">Juicebox jar (Unix, Windows, etc.)</a>
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.2.jar"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/javalogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.2.jar">Juicebox jar (Unix, Windows, etc.)</a>
 
 ## Version 1.6.1
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.1.exe"><img src="images/winlogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.1.exe">Juicebox for Windows</a>
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.1.exe"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/winlogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.1.exe">Juicebox for Windows</a>
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.1.dmg"><img src="images/maclogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.1.dmg">Juicebox for Mac</a>
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.1.dmg"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/maclogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.1.dmg">Juicebox for Mac</a>
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.1.jar"><img src="images/javalogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.1.jar">Juicebox jar (Unix, Windows, etc.)</a>
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.1.jar"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/javalogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.1.6.1.jar">Juicebox jar (Unix, Windows, etc.)</a>
 
 ## Version 1.5.2
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.exe"><img src="images/winlogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.exe">Juicebox for Windows</a>
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.exe"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/winlogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.exe">Juicebox for Windows</a>
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.dmg"><img src="images/maclogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.dmg">Juicebox for Mac</a>
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.dmg"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/maclogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.dmg">Juicebox for Mac</a>
 
-<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.jar"><img src="images/javalogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.jar">Juicebox jar (Unix, Windows, etc.)</a>
+<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.jar"><img src="https://raw.githubusercontent.com/wiki/aidenlab/Juicebox/images/javalogo.png" width=100 align="middle"/></a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicebox/Juicebox.jar">Juicebox jar (Unix, Windows, etc.)</a>