Merge remote-tracking branch 'mothur/master'

[mothur.git] / catchallcommand.cpp

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index 39cc44f86e2cbe70efba4cb2700ad3154eb91945..bf866cbedca07b7ee8b732eec683c64520ee2017 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -176,7 +176,7 @@ int CatchAllCommand::execute() {
                
                savedOutputDir = outputDir;
                string catchAllCommandExe = ""; 
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        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
@@ -213,7 +213,7 @@ int CatchAllCommand::execute() {
                        
                        //for each label the user selected
                        while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
+                               
                                                
                                if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
                                                m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
@@ -221,10 +221,10 @@ int CatchAllCommand::execute() {
                                                //create catchall input file from mothur's inputfile
                                                string filename = process(sabund, inputFileNames[p]);
                                                string outputPath = m->getPathName(filename);
-                                       
+                                                                                       
                                                //create system command
                                                string catchAllCommand = "";
-                                               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                                               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                                        catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
                                                #else
                                                        if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
@@ -266,10 +266,10 @@ int CatchAllCommand::execute() {
                                                //create catchall input file from mothur's inputfile
                                                string filename = process(sabund, inputFileNames[p]);
                                                string outputPath = m->getPathName(filename);
-                                               
+                                                                                       
                                                //create system command
                                                string catchAllCommand = "";
-                                               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                                               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                                        catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
                                                #else
                                                        if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }
@@ -334,7 +334,7 @@ int CatchAllCommand::execute() {
                                
                                //create system command
                                string catchAllCommand = "";
-                               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                        catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1";
                                #else
                                        if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); }