880ad5f5e5b759ac892553985d6ab3721452e870
max
  Thu Dec 11 16:58:34 2014 -0800
largely revamped beacon, refs #14393
diff --git src/hg/hgBeacon/README.txt src/hg/hgBeacon/README.txt
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+The GA4H beacon system http://ga4gh.org/#/beacon is a tiny little webservice
+that accepts a chromosome position and replies with "yes", "no" or "maybe"
+if it finds information in a data track. This is to allow queries from outside
+users on protected variants. If they find variants in someone's beacon, they
+then can contact the institution to get more information about it.
+
+Please read the GA4H page before concluding that this CGI is inefficient. It's
+inefficient, but the purpose of the system is not maximum data transfer, but
+just limited information, so as to not identify patients or at least make it
+quite hard to identify them.
+
+It's implemented as a CGI script (hgBeacon) which calls bigBedToBed and a set of
+.bb files.  No mysql is required and the data files live in the same directory
+as the script and the bigBedtoBed binary. The makefile copies everything
+together into cgi-bin/beacon/.  The overhead of calling a binary is very
+small. We do this quite often in hgGene.
+
+We don't have personal data at UCSC so the beacon in this directory serves
+primarily LOVD and HGMD, which we cannot distribute.  These tracks are also
+not in the table browser, but the beacon makes it possible to at least query
+the positions in some way. 
+
+To get usage info, run the CGI with no option, e.g.
+http://hgwdev-max.soe.ucsc.edu/cgi-bin/hgBeacon
+
+The CGI also accepts INSDC accessions instead of "chr1" or just "1". The
+mapping is stored in insdcToUcsc.tab. 
+
+The CGI currently only supports hg19.
+
+