[MOBY-guts] biomoby commit

[Paul Gordon]

gordonp
Mon Jul 30 09:54:05 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services
In directory dev.open-bio.org:/tmp/cvs-serv5629/src/main/ca/ucalgary/services

Modified Files:
	ACDService.java 
Log Message:
Updated library path inclusion for EMBOSS
moby-live/Java/src/main/ca/ucalgary/services ACDService.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/ACDService.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/ACDService.java	2007/04/18 15:53:58	1.3
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/services/ACDService.java	2007/07/30 13:54:05	1.4
@@ -102,7 +102,7 @@
 					       "Valid choices from this run are:" + paramChoices);
 	    }
 
-	    // Transform the buts of binary data into a MOBY object or collection
+	    // Transform the bits of binary data into a MOBY object or collection
 	    MobyDataInstance mdi = null;
 	    try{
 		mdi = mobyClient.getMobyObject(resultParts, mobyOutputTemplate);
@@ -307,15 +307,14 @@
      * @return the standard output of the command
      */
     private String runProgram(MobyDataJob request, String[] command, File workingDir, final byte[] input) throws Exception{
-	// TODO: ensure $embossRootDirName/lib is in the LD_LIBRARY_PATH, 
-	// what is the equivalent in Windows?
-	//for(String cmdpart:  command){
-	//    System.err.print(cmdpart+" ");
-	//}
-	//System.err.println("");
+	// Ensure $embossRootDirName/lib is in the LD_LIBRARY_PATH, 
+	// what is the equivalent in Windows?  Windows searches just PATH...
+	String libDir = embossRootDirName+File.separator+"lib";
 	final Process process = runtime.exec(command, 
 					     new String[]{"EMBOSS="+embossRootDirName,
-							  "EMBOSS_ACDROOT="+acdRootDirName},
+							  "EMBOSS_ACDROOT="+acdRootDirName,
+					                  "LD_LIBRARY_PATH="+libDir,
+					                  "PATH="+libDir},
 					     workingDir);
 	final OutputStream stdin = process.getOutputStream();
 	final InputStream stderr = process.getErrorStream();