Changes for PATRIC build

src/edu/vt/vbi/ci/pepr/alignment/MultipleSequenceAligner.java

@@ -293,7 +293,7 @@ public void setMuscleHostWorkingDir(String muscleHostWorkingDir) {
 	}
 
 	private void determineMusclePath() {
-		muscleHostMusclePath = ExecUtilities.getCommandPath("muscle");
+		muscleHostMusclePath = ExecUtilities.getCommandPath("muscle-3.6");
 	}
 
 	public void addMuscleOption(String opt) {

src/edu/vt/vbi/ci/pepr/tree/pipeline/HMMSetEnhancer.java

@@ -502,7 +502,7 @@ private class HMMSearchRunner implements Runnable {
 		private String hmmFileName;
 		private TextFile[] resultHolder;
 		private HMMResult[][] hmmResultHolder; 
-		boolean keepHMMSearchFiles = true;
+		boolean keepHMMSearchFiles = false;
 
 		public HMMSearchRunner(String hmmfileName, TextFile[] resultHolder,
 				HMMResult[][] hmmResultHolder) {

src/edu/vt/vbi/ci/pepr/tree/pipeline/PhyloPipeline.java

@@ -46,6 +46,7 @@
  */
 public class PhyloPipeline {
 
+	private static final int MINIMUM_GENOME_COUNT = 4;
 
 	private static Logger logger;
 	private static HashMap<String,String> commands;
@@ -254,6 +255,10 @@ public PhyloPipeline(String[] args) {
 		if(uniqueSpecies) {
 			homologySearchSequenceFiles = 
 					filterOutDuplicateSpecies(homologySearchSequenceFiles);
+			if(homologySearchSequenceFiles.length < MINIMUM_GENOME_COUNT) {
+				System.out.println("There are not enough unique species to use the unique species filter, so all genomes will be used.");
+				homologySearchSequenceFiles = inputSequenceFiles;
+			}
 			Arrays.sort(homologySearchSequenceFiles);
 		} else if(uniqueGenus) {
 			homologySearchSequenceFiles = 
@@ -525,22 +530,28 @@ private static String newickToPATRICJSON(String newickTree, String[] outgroupGen
 		String idOnlyNewick = newickTree;
 		BasicTree tree = new BasicTree(newickTree);
 		String[] leaves = tree.getLeaves();
+		ArrayList<String> idList = new ArrayList<String>(leaves.length);
 		HashMap<String,String> nameToId = new HashMap<String,String>();
 		HashSet<String> outgroup = new HashSet<String>();
 		for(String og: outgroupGenomes) {
 			String[] parts = og.split(delimiter);
 			outgroup.add(parts[nameIndex].replaceAll("_", " "));
 		}
 
+		JSONObject labelJSON = new JSONObject();
 		//verify that leaves are in <genome_name>@<genome_id> format
 		//extract genome name and genome id to make map
 		//replace leaves with just genome id
 		for(String leaf: leaves) {
 			if(leaf.contains(delimiter)) {
 				String[] parts = leaf.split(delimiter);
+				String name = parts[nameIndex].replaceAll("_", " "); 
+				String id = parts[idIndex];
 				idOnlyNewick = idOnlyNewick.replaceFirst(leaf, parts[idIndex]);
-				nameToId.put(parts[nameIndex].replaceAll("_", " "), parts[idIndex]);
-			}
+				nameToId.put(name, id);
+				labelJSON.put(id,name);
+				idList.add(id);
+		}
 		}
 
 		JSONObject outgroupJSON = new JSONObject();
@@ -559,14 +570,7 @@ private static String newickToPATRICJSON(String newickTree, String[] outgroupGen
 
 		infoJSON.put("taxon_name", taxonName);
 		infoJSON.put("taxon_rank", taxonRank);
-
-		JSONObject labelJSON = new JSONObject();
-		names = nameToId.keySet().toArray(new String[0]);
-		Arrays.sort(names);
-		for(String name: names) {
-			String id = nameToId.get(name);
-			labelJSON.put(id,name);
-		}
+		infoJSON.put("ids", idList);
 
 		JSONObject fullJSON = new JSONObject();
 		fullJSON.put("info", infoJSON);
@@ -752,7 +756,7 @@ public static void setCommandPaths() {
 		logger.info("bin directory: " + binDirName);
 
 		String[] commands = new String[]{
-				"muscle",
+				"muscle-3.6",
 				"Gblocks",
 				"blastall",
 				"blat",
@@ -770,11 +774,13 @@ public static void setCommandPaths() {
 				"hmmsearch"
 		};
 
+/*
 		for(int i = 0; i < commands.length; i++) {
 			String fullCommandPath = binDirName + commands[i];
 			logger.info("set path for '" + commands[i] + "' to '" + fullCommandPath + "'" );
 			System.setProperty(commands[i], fullCommandPath);
 		}
+		*/
 	}
 
 	private TextFile runMCL(TextFile hitPairFile, String inflation, int threads) {
@@ -1141,7 +1147,7 @@ private void checkForRequiredPrograms() {
 				"hmmbuild",
 				"hmmsearch",
 				"mcl",
-				"muscle",
+				"muscle-3.6",
 				"raxmlHPC",
 				"raxmlHPC-PTHREADS"
 		};

src/edu/vt/vbi/ci/util/CommandResults.java

@@ -14,11 +14,14 @@ public class CommandResults {
 
 	private String[] stdout;
 	private String[] stderr;
+    private int rc;
 
-	public CommandResults(String[] stdout, String[] stderr) {
+    public CommandResults(String[] stdout, String[] stderr, int rc) {
 		this.stdout = stdout;
 		this.stderr = stderr;
+		this.rc = rc;
 	}
+    public int getRc() { return rc; }
 
 	public String[] getStdout() {
 		return stdout;

src/edu/vt/vbi/ci/util/ExecUtilities.java

@@ -25,6 +25,11 @@ public static CommandResults exec(String command) {
 			logger.info(command);
 			Process proc = Runtime.getRuntime().exec(command);
 			r = getResultFromProcess(proc);
+			logger.info(command + " has rc " + r.getRc() + "\n");
+			for (String s : r.getStderr())
+			{
+			    logger.info("  " + s);
+			}
 		} catch (IOException e) {
 			e.printStackTrace();
 		} catch (InterruptedException e) {
@@ -52,6 +57,12 @@ public static CommandResults exec(String[] command) {
 			e.printStackTrace();
 		}
 
+		if (r.getRc() != 0)
+		{
+		    logger.warn("Error return " + r.getRc() + " from command " + command);
+		}
+
+
 		return r;
 	}
 
@@ -82,13 +93,14 @@ private static CommandResults getResultFromProcess(Process proc) throws Interrup
 
 		errorThread.join();
 		outThread.join();
-		r = new CommandResults(outReader.getLinesRead(),
-				errorRead.getLinesRead());
 
 		//call destroy() on process to free resources. The streams
 		//are not closed automatically, and may eventually 
 		//accumulate and result in an "IOException: Too many open files"
-		proc.waitFor();
+		int rc = proc.waitFor();
+		r = new CommandResults(outReader.getLinesRead(),
+				       errorRead.getLinesRead(), rc);
+
 		try {
 			proc.getErrorStream().close();
 			proc.getInputStream().close();