X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setdircommand.cpp;h=67a1f59f8388dbfec55ae7b552f02640b5d6b93f;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=3135b8133c851e5fe58a13ee32e29da05da90216;hpb=9d6f36294dcaef3ac65a0e69fd8140077c3209e0;p=mothur.git

diff --git a/setdircommand.cpp b/setdircommand.cpp
index 3135b81..67a1f59 100644
--- a/setdircommand.cpp
+++ b/setdircommand.cpp
@@ -59,6 +59,7 @@ SetDirectoryCommand::SetDirectoryCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -100,6 +101,14 @@ int SetDirectoryCommand::execute(){
 		
 		commandFactory = CommandFactory::getInstance();
 		
+		string tag = "";
+#ifdef USE_MPI
+		int pid; 
+		MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+		
+		tag = toString(pid);
+#endif
+		
 		m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
 		
 		//redirect output
@@ -121,14 +130,14 @@ int SetDirectoryCommand::execute(){
 			
 			//test to make sure directory exists
 			output = m->getFullPathName(output);
-			string outTemp = output + "temp";
+			string outTemp = output + tag + "temp";
 			ofstream out;
 			out.open(outTemp.c_str(), ios::trunc);
 			if(!out) {
 				m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine(); 
 			}else{
 				out.close();
-				remove(outTemp.c_str());
+				m->mothurRemove(outTemp);
 				m->mothurOut("outputDir=" + output); m->mothurOutEndLine();  
 				commandFactory->setOutputDirectory(output);
 			}
@@ -153,14 +162,14 @@ int SetDirectoryCommand::execute(){
 			
 			//test to make sure directory exists
 			input = m->getFullPathName(input);
-			string inTemp = input + "temp";
+			string inTemp = input + tag + "temp";
 			ofstream in;
 			in.open(inTemp.c_str(), ios::trunc);
 			if(!in) {
 				m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine(); 
 			}else{
 				in.close();
-				remove(inTemp.c_str());
+				m->mothurRemove(inTemp);
 				m->mothurOut("inputDir=" + input); m->mothurOutEndLine();  
 				commandFactory->setInputDirectory(input); 
 			}
@@ -193,8 +202,19 @@ int SetDirectoryCommand::execute(){
 				if (lastChar != "\\") { tempdefault += "\\"; }	
 			#endif
 			
-			m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();  
-			m->setDefaultPath(tempdefault);
+			//test to make sure directory exists
+			tempdefault = m->getFullPathName(tempdefault);
+			string inTemp = tempdefault + tag + "temp";
+			ofstream in;
+			in.open(inTemp.c_str(), ios::trunc);
+			if(!in) {
+				m->mothurOut(tempdefault + " directory does not exist or is not writable."); m->mothurOutEndLine(); 
+			}else{
+				in.close();
+				m->mothurRemove(inTemp);
+				m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();  
+				m->setDefaultPath(tempdefault);
+			}
 		}
 
 		return 0;