bc8309fd97790f92e99ad26c2a97626c8024fc0b
max
  Wed Nov 26 05:17:44 2014 -0800
additions to beacon readme, refs #14393
diff --git src/beacon/README.txt src/beacon/README.txt
index fedf636..d2bc66c 100644
--- src/beacon/README.txt
+++ src/beacon/README.txt
@@ -1,31 +1,36 @@
 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.
 
 It's implemented as a CGI script (query) which uses 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 data for the beacon, the .bb files, are copied into the cgi-bin directory
-from /hive/data/genomes/hg19/bed/beacon
-
 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/beacon/query
 
 The CGI keeps a list of counts of IP+date, to limit the maximum number of
 queries to 1000 a day. This is to make it harder to query the whole genome and
 identify a person from the responses. This limit can most likely be increased.
 
 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.
 
+Installation:
+The data for the beacon, the .bb files, are copied into the cgi-bin directory
+from /hive/data/genomes/hg19/bed/beacon
+The get a working beacon, one needs to copy the script ("query"), bigBedToBed,
+insdcToUcsc.tab, accCounts.gdbm and the four bigBed files:
+lovd.bb, hgmd.bb, spMut.bb and clinvarMain.bb. The makefile will do all the
+copying.
+