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/help.txt src/hg/hgBeacon/help.txt
new file mode 100644
index 0000000..45272eb
--- /dev/null
+++ src/hg/hgBeacon/help.txt
@@ -0,0 +1,45 @@
+<pre>
+A Genomics Alliance Beacon at UCSC, see http://ga4gh.org/#/beacon
+
+In collaboration with the Leiden Open Variation Database and Biobase/HGMD.
+
+parameters:
+- chromosome: 1 - 22, X, Y or M
+- position: 0-based position on chromosome
+- dataset: either lovd or hgmd. If not provided, queries both LOVD and HGMD.
+- reference: optional. if specified, has to be GRCh37
+- allele: A,C,T,G. Ignored for HGMD (HGMD gives out only
+  positions, not the alleles, these are only on their website)
+- format: if "text",  does not return JSON, but just one of the words "true",
+      "false" or "overlap".  Easier to parse for simple shell scripts.
+
+To get more details about a variant:
+- dataset lovd: Use the LOVD API to get all info, see chapter 9 of the 
+  LOVD manual, http://www.lovd.nl/3.0/docs/LOVD_manual_3.0.pdf
+  Or search manually on http://www.lovd.nl/3.0/home
+- dataset hgmd: Create an account on http://www.hgmd.cf.ac.uk/ and search
+  manually for the variant.
+
+Note that only single-basepair substitutions are available from both databases.
+Insertions and deletions might be available with later versions of the Beacon
+API.
+
+Examples:
+http://%(host)s/cgi-bin/hgBeacon/query?dataset=lovd&chromosome=1&position=808921&allele=T
+- returns "true"
+
+http://%(host)s/cgi-bin/hgBeacon/query?dataset=hgmd&chromosome=1&position=985954&allele=T
+- returns "true", for any allele, as HGMD does not share the alleles
+
+http://%(host)s/cgi-bin/beacon3/query?dataset=hgmd&chromosome=1&position=2160493&allele=T
+- returns "false", no information at this position
+
+IP-based throttling:
+For each incoming request from an IP address, 75 msecs are added after every
+request, and every 15 secs 75 seconds are removed. No delay is imposed when
+fewer than 10 seconds have accumulated. This means that about 150 queries
+can be sent before a delay of about 10 seconds is imposed for an IP
+address. If a delay of 20 seconds has accumulated (=the client is using
+multi-threaded requests) the client IP is blocked from further requests
+until the delay falls under 20 seconds.
+</pre>