added blastn

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3379 ee4ac58c-ac51-4696-9907-e4b3aa274f04

lib/j2ssh/j2ssh.properties

@@ -2,6 +2,7 @@ port=2222
 host=localhost
 bsub=bsub -q  longblastq -n 1 -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' 
 blastp=-I /nfs/pathsoft/prod/perl/flexi_blast.pl -p 
+blastn=-I /nfs/pathsoft/prod/perl/flexi_blast.pl
 fasta=-I /nfs/disk222/yeastpub/bio-soft/fasta/fasta33_t -B -S -q -b 100 -H -l /nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs
 %uniprot=%U
 %uniprot_archaea=%A

uk/ac/sanger/artemis/j2ssh/SshPSUClient.java

@@ -114,7 +114,9 @@ public class SshPSUClient extends Thread
     }
     if(cmd.equals("blastp") && settings.getProperty("blastp") != null)
       cmd = settings.getProperty("blastp");
-    if(cmd.equals("fasta") && settings.getProperty("fasta") != null)
+    else if(cmd.equals("blastn") && settings.getProperty("blastn") != null)
+      cmd = settings.getProperty("blastn");
+    else if(cmd.equals("fasta") && settings.getProperty("fasta") != null)
       cmd = settings.getProperty("fasta");
 
     try
@@ -237,10 +239,13 @@ public class SshPSUClient extends Thread
           if(index > -1)
             filename = filename.substring(index+1);
 
-          wdir = wdir+"/"+user+"/";
           try
           {
+            wdir = wdir+"/"+user;
             sftp.mkdir(wdir);
+            wdir = wdir+"/"+program+"/";
+            sftp.mkdir(wdir);
+
             sftp.put(filepath, wdir+filename);
           }
           catch(IOException ioe)
@@ -293,6 +298,7 @@ public class SshPSUClient extends Thread
               } 
               count++;
             }
+            Thread.currentThread().sleep(5000);
           }
           catch(InterruptedException ie)
           {
@@ -307,6 +313,7 @@ public class SshPSUClient extends Thread
           System.out.println(stdouth.getOutput());
           System.out.println(stderrh.getOutput());
 
+
 //        ByteArrayOutputStream os = new ByteArrayOutputStream();
 //        sftp.get(outputfile, os);
 //        System.out.println(os.toString());