Add me testing script

testing/run_server.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+if [ ! -d virus-zymo-kraken2 ]; then
+    echo " +++ Downloading database +++"
+    wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/misc/virus-zymo-kraken.tar.gz
+    tar -xzvf virus-zymo-kraken.tar.gz
+else
+    echo " +++ Database downloaded previously +++"
+fi
+
+echo ""
+if [ ! -d virus-zymo-kraken2.reads.fastq.gz ]; then
+    echo " +++ Downloading reads +++"
+    wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/misc/virus-zymo-kraken.reads.fastq.gz
+else
+    echo " +++ Reads downloaded previously +++"
+fi
+
+echo ""
+echo " +++ Starting a client before the server +++"
+../build/client/kraken2_client --port 8080 --host-ip 127.0.0.1 
+
+echo ""
+echo " +++ Starting server +++"
+../build/server/kraken2_server --db virus-zymo-kraken2 --host-ip 127.0.0.1 --wait 2 &
+sleep 5  # give database time to load
+
+echo ""
+echo " +++ Sending reads as stream +++"
+../build/client/kraken2_client --report "kraken.stream.report" --sequence virus-zymo-kraken.reads.gz --port 8080 --host-ip 127.0.0.1 \
+    | sort -k 2 > client.stream.classifications.fasta.txt
+
+echo ""
+echo " +++ Shutting down server +++ "
+../build/client/kraken2_client --port 8080 --shutdown
+
+#trap "trap - SIGTERM && kill -- -$$" SIGINT SIGTERM EXIT