X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=systemcommand.cpp;h=e5aeb3e8b73dfb59008f6ddccaa3b0703b25e696;hb=43835751a12097ea9d46a4ce68e2671ba7aff9d4;hp=129ed8012fe92aafe37ec8946a2f3367d3da79ce;hpb=4de093e3b92bdab1579565cb2873553412f6671e;p=mothur.git

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 129ed80..e5aeb3e 100644
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -91,7 +91,19 @@ int SystemCommand::execute(){
 		
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
-		system(command.c_str());
+		//system(command.c_str());
+		FILE *lsofFile_p = popen(command.c_str(), "r");
+		
+		if (!lsofFile_p) { return 0; }
+		
+		char buffer[1024];
+		while ( fgets(buffer, 1024, lsofFile_p) != NULL ) {
+			string temp = buffer;
+			m->mothurOut(temp); 
+		}
+		m->mothurOutEndLine();
+		
+		pclose(lsofFile_p);
 		
 		return 0;		
 	}