Third Party Server
******************

Configuration
=============

The Third Party Server must provide at least 2 scripts :

- one to get a public RSA Key for a Session
- one to launch a series of Association Tests

GetPublicRSAKey
---------------

Example For Simple Unix based System:

.. code-block:: bash

   #!/bin/bash
   
   if [ $# -lt 1 ]
   then
           echo -e "usage :\t$0 SessionID";
           exit 1;
   fi
   
   installDir=/path/to/PrivAS/WorkingDirectory
   jar=/path/to/PrivAS.TPS.VERSION.jar
   
   java -jar $jar --keygen $installDir/sessions $1

LaunchAssociationTest
---------------------

Example For Simple Unix based System:

.. code-block:: bash

   #!/bin/bash
   
   if [ $# -lt 1 ]
   then
           echo -e "usage :\t$0 SessionID";
           exit 1;
   fi
   
   session=$1
   installDir=/path/to/PrivAS/WorkingDirectory
   jar=/path/to/PrivAS.TPS.VERSION.jar
   core=24
   seed="random" #random seed for Production
   #seed="123456789" #fixed seed for Debugging
   d=`date +"%Y-%m-%d"`;
   log=$installDir/log/$d.log
   mkdir -p $installDir/sessions/$session;
   status=$installDir/sessions/$session/tps.status;
   epoch=`date +%s`000;
   echo -e "$epoch\tPENDING\tJob submitted from $HOSTNAME" >> $status;
   
   
   java -jar $jar "$session" "$installDir" "$core" "$seed" &>> $log

PrivAS TPS's Command Lines
==========================

Main Command
------------

Launch the Third-Party Server (should be called by the provided script, to manage scheduler issues)
...................................................................................................



.. code-block:: bash

   java -jar PrivAS.TPS.jar Session_ID Work_Directory Integer Long

+----------------+----------------------------------------------------------------------------+
| Session_ID     | the session ID used to generate the key pair                               |
+----------------+----------------------------------------------------------------------------+
| Work_Directory | The path to the directory where the keys will be stored                    |
+----------------+----------------------------------------------------------------------------+
| Integer        | Number of cores (actually threads) to use                                  |
+----------------+----------------------------------------------------------------------------+
| Long           | Initial seed for the random number generator (or "random" for random seed) |
+----------------+----------------------------------------------------------------------------+


Tools
-----

Generate a keypair for the Third-Party Server
.............................................



.. code-block:: bash

   java -jar PrivAS.TPS.jar --keygen Work_Directory Session_ID

+----------------+---------------------------------------------------------+
| Work_Directory | The path to the directory where the keys will be stored |
+----------------+---------------------------------------------------------+
| Session_ID     | the session ID used to generate the key pair            |
+----------------+---------------------------------------------------------+


Compute a WSS Association Test (locally)
........................................



.. code-block:: bash

   java -jar PrivAS.TPS.jar --wss genotype_files.tsv phenotypes.bool Integer Long results.tsv

+--------------------+-----------------------------------------------------------------------------------------------------------------------+
| genotype_files.tsv | A TSV file that lists the genotypes files to used as input (Column1: Gene Name, Column2: /path/to/the/file.genotypes) |
+--------------------+-----------------------------------------------------------------------------------------------------------------------+
| phenotypes.bool    | A TSV file that stores the phenotypes of the samples (0/false = unaffected, 1/true = affected                         |
+--------------------+-----------------------------------------------------------------------------------------------------------------------+
| Integer            | Number of cores (actually threads) to use                                                                             |
+--------------------+-----------------------------------------------------------------------------------------------------------------------+
| Long               | Initial seed for the random number generator (or "random" for random seed)                                            |
+--------------------+-----------------------------------------------------------------------------------------------------------------------+
| results.tsv        | TSV file that will store the result table                                                                             |
+--------------------+-----------------------------------------------------------------------------------------------------------------------+


Compute a WSS Ranksum
.....................



.. code-block:: bash

   java -jar PrivAS.TPS.jar --ranksum geneName input.genotypes phenotypes.bool

+-----------------+-----------------------------------------------------------------------------------------------+
| geneName        | The Name of the gene                                                                          |
+-----------------+-----------------------------------------------------------------------------------------------+
| input.genotypes | the path to the genotypes file to use as input                                                |
+-----------------+-----------------------------------------------------------------------------------------------+
| phenotypes.bool | A TSV file that stores the phenotypes of the samples (0/false = unaffected, 1/true = affected |
+-----------------+-----------------------------------------------------------------------------------------------+