880ad5f5e5b759ac892553985d6ab3721452e870
max
  Thu Dec 11 16:58:34 2014 -0800
largely revamped beacon, refs #14393
diff --git src/beacon/README.txt src/beacon/README.txt
deleted file mode 100644
index d2bc66c..0000000
--- src/beacon/README.txt
+++ /dev/null
@@ -1,36 +0,0 @@
-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/.
-
-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.
-