3ba0a1c2f2cb0b220a2989225ff9512d2531070b max Fri Dec 19 07:33:10 2014 -0800 changes after code review, refs #14545 diff --git src/hg/hgBeacon/README.txt src/hg/hgBeacon/README.txt index 5ad5a21..244d8a5 100644 --- src/hg/hgBeacon/README.txt +++ src/hg/hgBeacon/README.txt @@ -1,31 +1,31 @@ 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/hgBeacon +http://genome-test.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.