add usage

docs/index.rst

@@ -10,6 +10,7 @@ WashU Epigenome Browser
     :maxdepth: 2
     :caption: Contents:
 
+    usage
     tracks
     datahub
     installation

docs/tracks.rst

@@ -3,6 +3,59 @@ Tracks
 
 This following sections introduce the track types the browser supports.
 
+Prepare track files
+-------------------
+
+The browser access the track files from its URL, only the proportion of the data in
+the specific viewed region are transferred to the browser for visualization. Thur, all
+the track files need be hosted in a web accssible location use HTTP or HTTPS.
+
+Binary track file format like bigWig_ and HiC_ can be used directly with the browser.
+bedGraph_, methylC_ and categorical_ track files need 
+be `compressed by bgzip and indexed by tabix`_ for used by the browser.
+The resulted index file with suffix ``.tbi`` need be located
+at the same URL with the ``.gz`` file.
+
+Bed like format track files need be sorted first, say we have a track file named ``track.bedgraph``,
+we can use generic Linux ``sort`` command or the ``bedSort`` tool from UCSC. The following 2 commands
+do the same thing.
+
+    sort -k1,1 -k2,2n track.bedgraph > track.bedgraph.sorted
+or
+    bedSort track.bedgraph track.bedgraph.sorted
+
+then compressed and index using tabix:
+
+    bgzip track.bedgraph.sorted
+    tabix -p bed track.bedgraph.sorted.gz
+
+Move files "track.bedgraph.sorted.gz" and "track.bedgraph.sorted.gz.tbi" to a web server. 
+The two files must be in the same directory. Obtain the URL to "track.bedgraph.sorted.gz" for submission.
+
+.. _`compressed by bgzip and indexed by tabix`: http://www.htslib.org/doc/tabix.html
+
+Configure your webserver to enable CORS
+-------------------------------------
+
+Quoted from MDN_:
+
+    Cross-Origin Resource Sharing (CORS) is a mechanism that uses additional HTTP headers
+    to tell a browser to let a web application running at one origin (domain) 
+    have permission to access selected resources from a server at a different origin. 
+    A web application makes a cross-origin HTTP request when it requests a resource that
+    has a different origin (domain, protocol, and port) than its own origin.
+
+.. _MDN: https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS
+
+Since the browser domain is different with the server the tracks are hosted, the hosting server
+need enable CORS, for Apache web server in Ubuntu, this setup would work:
+
+    Header always set Access-Control-Allow-Origin "*"
+    Header always set Access-Control-Allow-Methods "POST, GET, OPTIONS, DELETE, PUT"
+    Header always set Access-Control-Max-Age "1000"
+    Header always set Access-Control-Allow-Headers "x-requested-with, Content-Type, origin, authorization, accept, client-security-token"
+
+
 Numerical Tracks
 ----------------
 
@@ -34,11 +87,31 @@ Example lines are below::
     chr12   6537600 6537601 29.30229
 
 Every line consists of 4 fields separated by ``Tab`` delimiter,the fields from
-left to right are ``chromosome``, ``start position``, ``end position`` (not included), and ``value``.
+left to right are ``chromosome``, ``start position`` (0-based), ``end position`` (not included), and ``value``.
 
 .. note:: You can use nagative values for reverse strand, both positive and negative
           values can exist in same coordinates (they can overlap), in ``bigWig`` format
           you can also specify negative values, but they cannot overlap with positive values.
 
 .. _UCSC bedGraph: https://genome.ucsc.edu/goldenpath/help/bedgraph.html
 
+Methylation tracks
+------------------
+
+methylC
+~~~~~~~
+
+Methylation data are formatted in ``methylC`` format, which is a 7 column bed format file.
+
+Categorical tracks
+------------------
+
+categorical
+~~~~~~~~~~~
+
+Long range chromatin interaction
+--------------------------------
+
+HiC
+~~~
+

docs/usage.rst

@@ -0,0 +1,71 @@
+Use the Browser
+===============
+
+Navigator to genomic regions
+----------------------------
+
+Jump to a Gene
+~~~~~~~~~~~~~~
+
+Voice input gene symbol
+^^^^^^^^^^^^^^^^^^^^^^^
+
+.. note:: The feature is dependent on web browser support, web browser without support for
+          speech recognition won't see this UI.
+
+Jump to a specific region
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Operations in tracks view container
+-----------------------------------
+
+Move/Zoom/Re-order tool
+~~~~~~~~~~~~~~~~~~~~~~~
+
+Default tool is `Move`.
+
+Undo/Redo/History tool
+~~~~~~~~~~~~~~~~~~~~~~
+
+Settings
+--------
+
+Toggle display of genome Navigator
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Toggle highlighting of enter region
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Change track lable width
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+Toggle display of VR mode
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Session
+-------
+
+Save session
+~~~~~~~~~~~~
+
+Retrieve session
+~~~~~~~~~~~~~~~~
+
+Live browsing
+-------------
+
+Screenshot
+----------
+
+Track management
+----------------
+
+Add tracks from public hubs
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Add custom tracks or data hub
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Also see tracks and datahub section for how to prepare your tracks and datahub file.
+
+