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:

#!/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:

#!/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)¶

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¶

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)¶

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¶

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