diff --git a/uk/ac/sanger/artemis/j2ssh/SshLogin.java b/uk/ac/sanger/artemis/j2ssh/SshLogin.java
index daad75e5f54da3d68aa15f2d5ed6b9929b779eff..1d736a5b791e0f81b2c37060b8fbc7387a4105f3 100644
--- a/uk/ac/sanger/artemis/j2ssh/SshLogin.java
+++ b/uk/ac/sanger/artemis/j2ssh/SshLogin.java
@@ -58,7 +58,6 @@ public class SshLogin
 {
   // defaults
   private String logfile  = null;
-  private String wdir     = "/nfs/pathscratch1/scratch";
 
   // login variables
   private String hostname = null;
diff --git a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
index c6ed411bf1e232aab13d277326415dee90e2feec..4126d85c6aaef353990905f78a8fe2863fc79837 100644
--- a/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
+++ b/uk/ac/sanger/artemis/j2ssh/SshPSUClient.java
@@ -212,6 +212,9 @@ public class SshPSUClient extends Thread
         db = "%uniprot";
     } 
 
+    if(settings.getProperty("wdir") != null)
+      wdir = settings.getProperty("wdir");
+
     if(cmd != null)
     {
       if(cmd.equals("blastp") && settings.getProperty("blastp") != null)