e1416402b095c32aca50aba19a3f7e75c2aa3412 max Thu Mar 5 16:16:31 2015 -0800 during its last code review, hgBeacon was criticized, partially, because it's calling bigBedInfo and bigBedToBed and so requires copies of these in the cgi-bin dir. This change makes hgBeacon easier to install as it does not need the external tools anymore. It also adds a tester that can be pointed at the hgBeacon to see if it works, at least the basic functions. It also makes it easier to import VCF files, as it can import these directly. diff --git src/hg/hgBeacon/README.txt src/hg/hgBeacon/README.txt index 244d8a5..42e7f96 100644 --- src/hg/hgBeacon/README.txt +++ src/hg/hgBeacon/README.txt @@ -1,31 +1,24 @@ 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. +The purpose of the system is not maximum data transfer, but limiting +information, so as to prevent the identification of patients or at least make +it quite hard to identify them. +It's implemented as a CGI script (hgBeacon) which stores the data in a sqlite +database under /gbdb/hg19/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. +not in the table browser, but the beacon makes it possible to query +their positions at least. To get usage info, run the CGI with no option, e.g. 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. - +API ref at +https://docs.google.com/document/d/154GBOixuZxpoPykGKcPOyrYUcgEXVe2NvKx61P4Ybn4