vector<string> dirs;
mout->splitAtChar(envPath, dirs, delim);
+ if (mout->debug) { mout->mothurOut("[DEBUG]: dir's in path: \n"); }
+
//get path related to mothur
for (int i = 0; i < dirs.size(); i++) {
+
+ if (mout->debug) { mout->mothurOut("[DEBUG]: " + dirs[i] + "\n"); }
+
//to lower so we can find it
string tempLower = "";
for (int j = 0; j < dirs[i].length(); j++) { tempLower += tolower(dirs[i][j]); }
//is this mothurs path?
if (tempLower.find("mothur") != -1) { mothurPath = dirs[i]; break; }
}
-
+
+ if (mout->debug) { mout->mothurOut("[DEBUG]: mothurPath = " + mothurPath + "\n"); }
+
if (mothurPath != "") {
//add mothur so it looks like what argv would look like
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
mout->openInputFile(tempIn, in, "");
//if this file exists
- if (in) { in.close(); mothurPath = tempIn; break; }
+ if (in) { in.close(); mothurPath = tempIn; break; if (mout->debug) { mout->mothurOut("[DEBUG]: found it, mothurPath = " + mothurPath + "\n"); } }
}
}