src/hg/encode/encodeCharts/README 1.4

Index: src/hg/encode/encodeCharts/README
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/encodeCharts/README,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/encode/encodeCharts/README	7 Apr 2010 23:15:39 -0000	1.3
+++ src/hg/encode/encodeCharts/README	2 Jun 2010 00:37:02 -0000	1.4
@@ -1,39 +1,42 @@
 *) README
 
-*) encodeTimeline.py
-   Now a cgi-bin python script.
+Suite of CGI scripts that visualize the data in the latest report file
+found in: /hive/groups/encode/dcc/reports
 
-   Notes: Uses the 2.6 version of python 
-            #!/hive/groups/recon/local/bin/python
-          Requires the gviz_api.py library
-
-*) Deprecated - encodeTimeline.py [No longer a command-line program]
-
-Run the program:
-  $ encodeTimeline.py > timeline.html
-
-  The program has hard-coded paths for 
-    the report directory
-    the important dates file
-
-  The program finds the most recent report file, parses it and
-  outputs an html file where the data is stored statically via Javascript.
+The Visualization API used is the Google Visualization API:
+  http://code.google.com/apis/visualization/interactive_charts.html
 
-*) Deprecated Instructions using old Perl script
+File structure when properly installed:
 
-Run the program:
+In the "/hive/groups/encode/dcc/charts" dir:
+	important.dates.tab
+		tab-delimited file that lists the freeze dates
+	gviz_api.py
+		Google Viz API Python module
+		http://code.google.com/apis/visualization/documentation/dev/gviz_api_lib.html
+	encodeReportLib.py
+		Python module of shared functions for ENCODE Report charts
+
+Installed in CGI-BIN directory:
+	encodeReport.py
+		Outputs the report file as raw text or as a spreadsheet
+	encodeTimeline.py
+		Outputs the releases and submissions as a timeline
+	encodeStatus.py
+		Bar chart of the submission status
+	encodeReportFilter.py
+		Shows the associated rows given filtering criteria
+	encodeDist.py
+		Outputs the amount of time until release
+	encodeDistUnrelease.py
+		Outputs the amount of time since submission
 
-  $ encodeChart.pl newreport.2010-03-31.dcc.txt important.dates.tab > tab.out
+*) The charts are all linked from the ENCODE wiki page here:
 
-Logon to: http://docs.google.com
+  http://encodewiki.ucsc.edu/EncodeDCC/index.php/ENCODE_Report_Charts
 
-Open the file: ENCODE Cumulative Submit and Release
-
-Copy and paste file "tab.out" into the spreadsheet
-
-Chart should be automatically updated
-
-
-Send any questions and comments to:
-  Bernard Suh, bsuh@soe.ucsc.edu
+*) Additional notes
 
+Uses the 2.6 version of python 
+  The first line of all the scripts is:
+    #!/hive/groups/recon/local/bin/python