- 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
- if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); }
- else if (output == "default") {
- string exepath = m->argv;
- output = exepath.substr(0, (exepath.find_last_of('m')));
-
- m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
- commandFactory->setOutputDirectory(output);
- }else {
- //add / to name if needed
- string lastChar = output.substr(output.length()-1);
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- if (lastChar != "/") { output += "/"; }
- #else
- if (lastChar != "\\") { output += "\\"; }
- #endif
-
- //test to make sure directory exists
- output = m->getFullPathName(output);
- 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();
- m->mothurRemove(outTemp);
- m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
- commandFactory->setOutputDirectory(output);
- }
- }
-
- //redirect input
- if ((input == "clear") || (input == "")) { input = ""; commandFactory->setInputDirectory(input); }
- else if (input == "default") {
- string exepath = m->argv;
- input = exepath.substr(0, (exepath.find_last_of('m')));
-
- m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
- commandFactory->setInputDirectory(input);
- }else {
- //add / to name if needed
- string lastChar = input.substr(input.length()-1);
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- if (lastChar != "/") { input += "/"; }
- #else
- if (lastChar != "\\") { input += "\\"; }
- #endif
-
- //test to make sure directory exists
- input = m->getFullPathName(input);
- 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();
- m->mothurRemove(inTemp);
- m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
- commandFactory->setInputDirectory(input);
- }
- }
-
- //set default
- if (tempdefault == "clear") {
- #ifdef MOTHUR_FILES
- string temp = MOTHUR_FILES;
- m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine();
+ if (debugOnly) { }
+ else {
+ commandFactory = CommandFactory::getInstance();
+
+ m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
+
+ //redirect output
+ if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); }
+ else if (output == "default") {
+ string exepath = m->argv;
+ output = exepath.substr(0, (exepath.find_last_of('m')));
+
+ m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
+ commandFactory->setOutputDirectory(output);
+ }else {
+ if (m->dirCheck(output)) {
+ m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
+ commandFactory->setOutputDirectory(output);
+ }
+ }
+
+ //redirect input
+ if ((input == "clear") || (input == "")) { input = ""; commandFactory->setInputDirectory(input); }
+ else if (input == "default") {
+ string exepath = m->argv;
+ input = exepath.substr(0, (exepath.find_last_of('m')));
+
+ m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
+ commandFactory->setInputDirectory(input);
+ }else {
+ if (m->dirCheck(input)) {
+ m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
+ commandFactory->setInputDirectory(input);
+ }
+ }
+
+ //set default
+ if (tempdefault == "clear") {
+#ifdef MOTHUR_FILES
+ string temp = MOTHUR_FILES;
+ m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine();