fixed catchall PATH variable bug added trimera to chimera.slayer

[mothur.git] / catchallcommand.cpp

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index a462bc7df80d0a0543c6cf9722daeabf4159ca40..b0ab7c8314ac7e1a5b267b02bf2ccad559b62355 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -176,22 +176,24 @@ int CatchAllCommand::execute() {
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               //prepare full output directory
-               outputDir = m->getFullPathName(outputDir);
-               
                //get location of catchall
                GlobalData* globaldata = GlobalData::getInstance();
                path = globaldata->argv;
-               path = path.substr(0, (path.find_last_of('m')));
+               path = path.substr(0, (path.find_last_of("othur")-5));
                path = m->getFullPathName(path);
-
+               
                string catchAllCommandExe = ""; 
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                        catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
+                       if (outputDir == "") { outputDir = "./"; } //force full pathname to be created for catchall, this is necessary because if catchall is in the path it will look for input file whereever the exe is and not the cwd.
                #else
                        catchAllCommandExe += "\"" + path + "CatchAllcmdW.exe\"" + " ";
+                       if (outputDir == "") { outputDir = ".\\"; } //force full pathname to be created for catchall, this is necessary because if catchall is in the path it will look for input file whereever the exe is and not the cwd.
                #endif
                
+               //prepare full output directory
+               outputDir = m->getFullPathName(outputDir);
+               
                vector<string> inputFileNames;
                if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile);  globaldata->setFormat("sabund");  }
                else {  inputFileNames.push_back(sabundfile);  }                
@@ -237,7 +239,8 @@ int CatchAllCommand::execute() {
                                                        //wrap entire string in ""
                                                        catchAllCommand = "\"" + catchAllCommand + "\"";
                                                #endif
-                                                                               //run catchall
+                                       
+                                               //run catchall
                                                system(catchAllCommand.c_str());
                                        
                                                remove(filename.c_str());