diff --git a/autoscale.sh b/autoscale.sh
index 688bc46..3e9a4db 100755
--- a/autoscale.sh
+++ b/autoscale.sh
@@ -2,7 +2,7 @@
 
 
 JS2AUTOSCALING="/home/ubuntu/t-rex-monitor/js2-autoscaling.sh"
-CONFIG="/home/ubuntu/crux/crux/vars/crux_vars.sh"
+CONFIG="/home/ubuntu/t-rex/crux/vars/crux_vars.sh"
 SETUP_CONFIG="/home/ubuntu/t-rex-monitor/vm_vars.sh"
 QUEUES=("/etc/ben/queue/qc.ini" "/etc/ben/queue/assign.ini" "/etc/ben/queue/assignxl.ini" "/etc/ben/queue/ecopcr.ini" "/etc/ben/queue/blast.ini" "/etc/ben/queue/ac.ini" "/etc/ben/queue/newick.ini" "/etc/ben/queue/tronko.ini")
 
diff --git a/main/crux-pssh.sh b/main/crux-pssh.sh
index 7280f50..5c206ea 100755
--- a/main/crux-pssh.sh
+++ b/main/crux-pssh.sh
@@ -29,15 +29,15 @@ if [ "$(wc -l < tmphost)" -eq 1 ]; then
     host=$(cat tmphost)
 
     if [ "$BRANCH" = "master" ]; then
-        ssh "$host" "git clone https://github.com/CALeDNA/crux.git"
+        ssh "$host" "git clone https://github.com/eDNA-Explorer/t-rex.git"
     else
-        ssh "$host" "git clone -b $BRANCH https://github.com/CALeDNA/crux.git"
+        ssh "$host" "git clone -b $BRANCH https://github.com/eDNA-Explorer/t-rex.git"
     fi
 
-    scp "$CONFIG" "$host:/home/$USER/crux/crux/vars/"
+    scp "$CONFIG" "$host:/home/$USER/t-rex/crux/vars/"
 
     if [ "$ASSIGN" = "TRUE" ]; then
-        scp ./.env $host:/home/$USER/crux/tronko/assign/jwt/.env
+        scp ./.env $host:/home/$USER/t-rex/tronko/assign/jwt/.env
     fi
 
     ssh "$host" "sudo apt install awscli -y"
@@ -49,16 +49,16 @@ if [ "$(wc -l < tmphost)" -eq 1 ]; then
     fi
 else
     if [ "$ASSIGN" = "TRUE" ]; then
-        parallel-scp -h tmphost ./.env /home/$USER/crux/tronko/assign/jwt/.env
+        parallel-scp -h tmphost ./.env /home/$USER/t-rex/tronko/assign/jwt/.env
     fi
 
     if [ "$BRANCH" = "master" ]; then
-        parallel-ssh -i -t 0 -h tmphost "git clone https://github.com/CALeDNA/crux.git"
+        parallel-ssh -i -t 0 -h tmphost "git clone https://github.com/eDNA-Explorer/t-rex.git"
     else
-        parallel-ssh -i -t 0 -h tmphost "git clone -b $BRANCH https://github.com/CALeDNA/crux.git"
+        parallel-ssh -i -t 0 -h tmphost "git clone -b $BRANCH https://github.com/eDNA-Explorer/t-rex.git"
     fi
 
-    parallel-scp -h tmphost $CONFIG /home/$USER/crux/crux/vars/
+    parallel-scp -h tmphost $CONFIG /home/$USER/t-rex/crux/vars/
 
     parallel-ssh -i -t 0 -h tmphost "sudo apt install awscli -y"
 
diff --git a/vm_setup.sh b/vm_setup.sh
index b30b9d1..9d7d239 100755
--- a/vm_setup.sh
+++ b/vm_setup.sh
@@ -14,7 +14,7 @@ PRIMERS=""
 START=0
 NODES=0
 BENSERVER=""
-VARS="/home/ubuntu/crux/crux/vars/crux_vars.sh"
+VARS="/home/ubuntu/t-rex/crux/vars/crux_vars.sh"
 DASHBOARD=/var/lib/grafana/dashboards/overview.json
 while getopts "u:f:i:k:j:n:m:b:s:w:v:c:p:o:e:" opt; do
     case $opt in