//#include "uc.h"
#include "sequence.hpp"
#include "referencedb.h"
-
+#include "systemcommand.h"
//**********************************************************************************************************************
vector<string> ChimeraUchimeCommand::setParameters(){
string uchimeCommand;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
uchimeCommand = path + "uchime"; // format the database, -o option gives us the ability
+ if (m->debug) {
+ m->mothurOut("[DEBUG]: Uchime location using \"which uchime\" = ");
+ Command* newCommand = new SystemCommand("which uchime"); m->mothurOutEndLine();
+ newCommand->execute();
+ delete newCommand;
+ m->mothurOut("[DEBUG]: Mothur's location using \"which mothur\" = ");
+ newCommand = new SystemCommand("which mothur"); m->mothurOutEndLine();
+ newCommand->execute();
+ delete newCommand;
+ }
#else
uchimeCommand = path + "uchime.exe";
#endif
-
+
//test to make sure uchime exists
ifstream in;
uchimeCommand = m->getFullPathName(uchimeCommand);