update deploy script

deploy.sh

@@ -8,20 +8,20 @@
 APP_IMG="gitlab-registry.in2p3.fr/ifb-biosphere/apps/long_read_assembly:master"
 
 # Tuning if site proxy or not
-CLOUD_SERVICE = $(ss-get cloudservice)
+#CLOUD_SERVICE = $(ss-get cloudservice)
 #CLOUD_SERVICE="ifb-genouest-genostack"
 
-HOST_NAME=$( ss-get --timeout=3 hostname )
-#HOST_NAME="192.168.100.49"
-if [ "$CLOUD_SERVICE" == "ifb-genouest-genostack" ]; then
+#HOST_NAME=$( ss-get --timeout=3 hostname )
+HOST_NAME="192.168.100.49"
+#if [ "$CLOUD_SERVICE" == "ifb-genouest-genostack" ]; then
     # Cloud site WITH a site proxy
-    APP_PORT=80
-    PROXIED_IP=$( echo $HOST_NAME | sed "s|\.|-|g")
-    HOST_NAME="openstack-${PROXIED_IP}.genouest.org"
-    HTTP_ENDP="https://$HOST_NAME"
+#    APP_PORT=80
+#    PROXIED_IP=$( echo $HOST_NAME | sed "s|\.|-|g")
+#    HOST_NAME="openstack-${PROXIED_IP}.genouest.org"
+#    HTTP_ENDP="https://$HOST_NAME"
 
-    systemctl stop nginx
-else
+#    systemctl stop nginx
+#else
     # Cloud site WOUT a site proxy
     APP_PORT=8787
     HTTP_ENDP="https://$HOST_NAME"
@@ -48,7 +48,7 @@ else
 
     systemctl restart nginx
     systemctl enable nginx
-fi
+#fi
 
 # Docker volumes
 
@@ -66,17 +66,23 @@ while IFS=" :" read VOL_NAME VOL_TYPE VOL_IP VOL_DEV ; do
 done < /etc/auto.ifb_share
 IFS=$IFS_ORI
 
+# MBB Workflows reads data from /Data and write results to /Results
+mkdir ${VOL_DEV}/Data
+mkdir ${VOL_DEV}/Results
+DOCK_VOL+=" --mount type=bind,src=$VOL_DEV/Data,dst=/Data"
+DOCK_VOL+=" --mount type=bind,src=$VOL_DEV/Results,dst=/Results"
+
 # Run docker environment
 # pull from docker hub or comment following 2 lines if using a local registry
-docker pull mmassaviol/long_read_assembly
+#docker pull mmassaviol/long_read_assembly
 APP_IMG="long_read_assembly"
 
-CONTAINER_ID=$( docker run -d -p $APP_PORT:8787 $APP_IMG )
+CONTAINER_ID=$( docker run -d -p $APP_PORT:3838 $DOCK_VOL $APP_IMG )
 #docker exec --user rstudio $CONTAINER_ID bash -c 'ln -s /ifb/data/ $HOME/data'
 #docker exec --user rstudio $CONTAINER_ID bash -c 'rm -r $HOME/kitematic'
 
 # Set service URLs
 #echo $HTTP_ENDP
 #echo $RST_PASSWORD
-ss-set url.service "${HTTP_ENDP}"
-ss-set ss:url.service "[HTTPS]$HTTP_ENDP"
+#ss-set url.service "${HTTP_ENDP}"
+#ss-set ss:url.service "[HTTPS]$HTTP_ENDP"