Merge branch 'master' of gitlab.isb-sib.ch:ST/ga4gh-arraymap

README.md

-Beacon queries and interface for the MongoDB based _arrayMap_ cancer genome repository.
+Beacon queries and interface for the MongoDB based _[arrayMap](http://arraymap.org/ "arrayMap, visualizing cancer genome array data")_ cancer genome repository.
+
+The structure of the project is the following:
 
-Queries are contained inside the directory [mongo-queries](mongo-queries)
 
-An alternative would be to transform the native _arrayMap_ data format into VCF, and to use [the Python Simple Beacon Server](https://github.com/maximilianh/ucscBeacon).
+# mongo-queries:
+
+Queries are contained inside the directory [mongo-queries](mongo-queries)
 
 #### Download commands
 
 The following command can be used to download a chunk of the _arrayMap_ dataset, e.g. to understand data structures.
 
-```wget "http://arraymap.org/api/?db=arraymap&qcveto=1&api_out=samples&icdm_m=8,9&api_doctype=jsondata&randno=200" -O 200samples.json```
+```
+wget "http://arraymap.org/api/?db=arraymap&qcveto=1&api_out=samples&icdm_m=8,9&api_doctype=jsondata&randno=200" -O 200samples.json
+```
 
 The next command would replace the current local _arrayMap_ instance with the downloaded file.
 
-```mongoimport --drop --db arraymap --collection samples < 200samples.json --batchSize 1```
+```
+mongoimport --drop --db arraymap --collection samples < 200samples.json --batchSize 1
+```
+
+# beacon-app
+
+The directory contains the Beacon application itself. 
+
+The application is based on node and angular.
+
+In order to run the application on your localhost, you need to have [npm](https://www.npmjs.com/ "Package manager for JavaScript") installed.
+
+Then, run:
+
+```
+npm install
+```
+
+in order to get all the required Javascript packages (as listed in package.json), and then:
+
+```
+npm start
+```
+
+You should also have a __arrayMap__ MongoDB running on your __localhost__, on port __27017__ (see above).
+
+This can be changed in the application container:
+
+```
+app.js
+```
+
+#### bin
+
+Contains the www script which is used by 
+
+```
+npm start
+```
+
+to start the server.
+
+#### arraymap-beacon
+
+Contains the implementation of the Beacon API. There is one sub-directory per API version.
+
+#### test
+
+Contains the functional tests (based on the [Chai](http://chaijs.com/ "Chai assertion library for node" ) assertion library).
+
+#### public
+
+Contains the scripts, CSS, images, HTML for the UI part.
+
+#### routes
+
+Contains the routing script.