A GA4GH Draft Beacon implementation
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cherrypy
data
test
utils
README.md
beacon.conf
beaconData.GRCh37.sqlite
help.txt
index.html
info
query
testBeacon

README.md

Introduction

The GA4H beacon system http://ga4gh.org/#/beacon is a small webservice that accepts a chromosome position and allele and replies with "true" or "false. This is an implementation of the GA4GH beacon 0.2 draft API which tries to be as simple as possible to install and configure, it requires only Python >2.5, the default in current linux distributions and OSX.

For security reasons, the script is small and either provides its own webserver or runs within your existing webserver as a CGI. This beacon can slow down queries if too many come in from the same IP address, to prevent that someone queries the whole genome (see the end of this document). For security reasons, your raw data, like VCF (see below) are not accessed by the script, but first converted into the minimal format chrom-position-alternateBases.

Quick-start using the built-in webserver

This should work in OSX, Linux or Windows when Python is installed (in Windows you need to rename query to query.py):

git clone https://github.com/maximilianh/ucscBeacon.git 
cd ucscBeacon
./query -p 8888

Then go to your web browser and try a few URLs:

Stop the beacon server by hitting Ctrl+C.

Reset the databse and import your own data in VCF format (see below for other supported formats):

rm beaconData.GRCh37.sqlite
./query GRCh37 test yourData.vcf.gz

Restart the server:

./query -p 8888

And query again with URLs, as above, but adapting the chromosome and position to one that is valid in your dataset.

You can adapt the name of your beacon, your institution etc. by editing the file beacon.conf and change the beacon help text by editing the file help.txt

Installation in Apache as a CGI

On Ubuntu/Debian:

sudo apt-get install apache2 git
sudo a2enmod cgi
sudo service apache2 restart
cd /usr/lib/cgi-bin
git clone https://github.com/maximilianh/ucscBeacon.git 

On Centos/Fedora/Redhat:

sudo yum install httpd git
cd /var/www/cgi-bin
git clone https://github.com/maximilianh/ucscBeacon.git 

On OSX (thanks to Patrick Leyshock and Andrew Zimmer):

# Uncomment this line in /etc/apache2/httpd.conf
# "LoadModule cgi_module libexec/apache2/mod_cgi.so"
sudo apachctl -k restart
cd /Library/WebServer/CGI-Executables/
curl -L -G https://github.com/maximilianh/ucscBeacon/archive/master.zip -o beacon.zip
unzip beacon.zip

Test it

Usage help info (as shown at UCSC):

wget 'http://localhost/cgi-bin/ucscBeacon/query' -O -

or alternatively with curl, e.g. on OSX:

curl http://localhost/cgi-bin/ucscBeacon/query

Some test queries against the ICGC sample that is part of the repo:

wget 'http://localhost/cgi-bin/ucscBeacon/query?chromosome=1&position=10150&alternateBases=A&format=text' -O -
wget 'http://localhost/cgi-bin/ucscBeacon/query?chromosome=10&position=4772339&alternateBases=T&format=text' -O -

or alternatively using curl, e.g. on OSX:

curl 'http://localhost/cgi-bin/ucscBeacon/query?chromosome=1&position=10150&alternateBases=A&format=text'
curl 'http://localhost/cgi-bin/ucscBeacon/query?chromosome=10&position=4772339&alternateBases=T&format=text'

Both should display "true".

Test if the "info" symlink to the script works which shows some basic info about the beacon which you can adapt to your institution as needed:

wget 'http://localhost/cgi-bin/ucscBeacon/info' -O -

See 'Apache setup' below if this shows an error.

For easier usage, the script supports a parameter 'format=text' which prints only one word (true or false). If you don't specify it, the result will be returned as a JSON string, which includes the query parameters:

wget 'http://localhost/cgi-bin/ucscBeacon/query?chromosome=10&position=9775129&alternateBases=T' -O -

You can rename the "ucscBeacon" directory to any different name, like "beacon" or "myBeacon".

Adding your own data

Remove the default test database:

mv beaconData.GRCh37.sqlite beaconData.GRCh37.sqlite.old

Import some of the provided test files in complete genomics format:

./query GRCh37 testDataCga test/var-GS000015188-ASM.tsv test/var-GS000015188-ASM2.tsv -f cga

Or import some of the provided test files in complete genomics format:

./query GRCh37 testDataVcf test/icgcTest.vcf test/icgcTest2.vcf

Or import your own VCF file as a dataset 'icgc':

./query GRCh37 icgc simple_somatic_mutation.aggregated.vcf.gz

You can specify multiple filenames, so the data will get merged. A typical import speed is 100k rows/sec, so it can take a while if you have millions of variants.

You should now be able to query your new dataset with URLs like this:

wget "http://localhost/cgi-bin/ucscBeacon/query?chromosome=1&position=1234&alternateBases=T" -O -

By default, the beacon will check all datasets, unless you provide a dataset name, like this:

wget "http://localhost/cgi-bin/ucscBeacon/query?chromosome=1&position=1234&alternateBases=T&dataset=icgc" -O -

Note that external beacon users cannot query the database during the import.

Apart from VCF, the program can also parse the complete genomics variants format, BED format of LOVD and a special format for the database HGMD. You can run the 'query' script from the command line for a list of the import options.

Apache setup

If your apache does not allow symlinks or you cannot or do not want to modify the apache config, just use a hard link instead of a symlink:

rm info
ln query info

If you want to use the /info symlinks, you will need to allow symlinks in Apache. The Apache config file is /etc/httpd/conf/httpd.conf on Redhat and /etc/apache2/sites-enabled/000-default.conf on Debian/Ubuntu. The config line for this is "Options +SymLinksIfOwnerMatch", add it for the directory that contains cgi-bin or has the ExecCGI Option already set. See below for an example of what this should look like.

If you do not have a cgi-bin directory in Apache at all, you can create one by adding a section like the following to your apache config. The config is located in /etc/apache2/sites-enabled/000-default.conf in Debian-Ubuntu or /etc/httpd/httpd.conf in Redhat-like distros.

This what it should look like in distros still using Apache2.2, like CentOs/Redhat RHEL6:

ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
<Directory "/usr/lib/cgi-bin">
Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
Order allow,deny
Allow from all
</Directory>

This is the same for Apache2.4, for more modern distros like Ubuntu, Debian, ArchLinux, etc:

ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
<Directory "/usr/lib/cgi-bin">
Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
Require all granted
</Directory>

Restart Apache:

sudo apachectl -k restart

You can replace /usr/lib/cgi-bin with any other directory you prefer.

The index.html page

There is a page index.html in case you want a nicer user interface to your beacon. The beacon is not supposed to be used by humans, as it is an API but you may still want to show a nice form to query it. To do this, copy the index.html to the root of your web server, e.g. /var/www/html (Ubuntu/Redhat). You will have to adapt this line

<form action="/cgi-bin/ucscBeacon/query" method="get">

and replace /cgi-bin/ucscBeacon/query with the location of the query script on your web server.

The utils/ directory

The binary "bottleneck" tool in this directory is a static 64bit file distributed by UCSC.

It can be downloaded for other platforms from http://hgdownload.cse.ucsc.edu/admin/exe/ or compiled from source, see http://genome.ucsc.edu/admin/git.html .

IP throttling

The beacon can optionally slow down requests, if too many come in from the same IP address. This is meant to prevent whole-genome queries for all alleles. You have to run a bottleneck server for this, the tool is called "bottleneck". You can find a copy in the utils/ directory, or can download it as a binary from http://hgdownload.cse.ucsc.edu/admin/exe/ or in source from http://genome.ucsc.edu/admin/git.html. Run it as "bottleneck start", the program will stay as a daemon in the background.

Create a file hg.conf in the same directory as hgBeacon and add these lines:

bottleneck.host=localhost
bottleneck.port=17776

For each request, hgBeacon will contact the bottleneck server. It will increase a counter by 150msec for each request from an IP. After every second without a request from an IP, 10msec will get deducted from the counter. As soon as the total counter exceeds 10 seconds for an IP, all beacon replies will get delayed by the current counter for this IP. If the counter still exceeds 20 seconds (which can only happen if the client uses multiple threads), the beacon will block this IP address until the counter falls below 20 seconds again.