Changed back to xcode build.

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 34bc7d9f0cd60ae34f4ba5c6831f78cf5b32851b..7a32b803547870fb6ad5c2f96f8a7835504fd1b7 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -8,6 +8,7 @@
 
 /* Begin PBXBuildFile section */
                8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6A0FF2C0290799A04C91782 /* mothur.1 */; };
+               A70332B712D3A13400761E33 /* makefile in Sources */ = {isa = PBXBuildFile; fileRef = A70332B512D3A13400761E33 /* makefile */; };
                A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B64F12D37EC300DA6239 /* ace.cpp */; };
                A7E9B88212D37EC400DA6239 /* aligncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65112D37EC300DA6239 /* aligncommand.cpp */; };
                A7E9B88312D37EC400DA6239 /* alignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65312D37EC300DA6239 /* alignment.cpp */; };
@@ -295,7 +296,8 @@
 /* End PBXCopyFilesBuildPhase section */
 
 /* Begin PBXFileReference section */
-               8DD76FB20486AB0100D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; };
+               8DD76FB20486AB0100D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; };
+               A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
                A7E9B64F12D37EC300DA6239 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
                A7E9B65012D37EC300DA6239 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
                A7E9B65112D37EC300DA6239 /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = "<group>"; };
@@ -885,6 +887,7 @@
                08FB7795FE84155DC02AAC07 /* Source */ = {
                        isa = PBXGroup;
                        children = (
+                               A70332B512D3A13400761E33 /* makefile */,
                                A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */,
                                A7E9BA4F12D398D700DA6239 /* clearcut */,
                                A7E9B69812D37EC400DA6239 /* cluster.cpp */,
@@ -980,7 +983,7 @@
                1AB674ADFE9D54B511CA2CBB /* Products */ = {
                        isa = PBXGroup;
                        children = (
-                               8DD76FB20486AB0100D96B5E /* mothur */,
+                               8DD76FB20486AB0100D96B5E /* Mothur */,
                        );
                        name = Products;
                        sourceTree = "<group>";
@@ -1534,9 +1537,9 @@
 /* End PBXGroup section */
 
 /* Begin PBXNativeTarget section */
-               8DD76FA90486AB0100D96B5E /* mothur */ = {
+               8DD76FA90486AB0100D96B5E /* Mothur */ = {
                        isa = PBXNativeTarget;
-                       buildConfigurationList = 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "mothur" */;
+                       buildConfigurationList = 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */;
                        buildPhases = (
                                8DD76FAB0486AB0100D96B5E /* Sources */,
                                8DD76FAD0486AB0100D96B5E /* Frameworks */,
@@ -1546,10 +1549,10 @@
                        );
                        dependencies = (
                        );
-                       name = mothur;
+                       name = Mothur;
                        productInstallPath = "$(HOME)/bin";
                        productName = mothur;
-                       productReference = 8DD76FB20486AB0100D96B5E /* mothur */;
+                       productReference = 8DD76FB20486AB0100D96B5E /* Mothur */;
                        productType = "com.apple.product-type.tool";
                };
 /* End PBXNativeTarget section */
@@ -1571,7 +1574,7 @@
                        projectDirPath = "";
                        projectRoot = "";
                        targets = (
-                               8DD76FA90486AB0100D96B5E /* mothur */,
+                               8DD76FA90486AB0100D96B5E /* Mothur */,
                        );
                };
 /* End PBXProject section */
@@ -1852,6 +1855,7 @@
                                A7E9B98D12D37EC400DA6239 /* weighted.cpp in Sources */,
                                A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */,
                                A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */,
+                               A70332B712D3A13400761E33 /* makefile in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
@@ -1868,7 +1872,7 @@
                                GCC_MODEL_TUNING = G5;
                                GCC_OPTIMIZATION_LEVEL = 0;
                                INSTALL_PATH = /usr/local/bin;
-                               PRODUCT_NAME = mothur;
+                               PRODUCT_NAME = Mothur;
                        };
                        name = Debug;
                };
@@ -1881,7 +1885,7 @@
                                GCC_MODEL_TUNING = G5;
                                GCC_WARN_UNUSED_VALUE = YES;
                                INSTALL_PATH = ./;
-                               PRODUCT_NAME = mothur;
+                               PRODUCT_NAME = Mothur;
                        };
                        name = Release;
                };
@@ -1952,7 +1956,7 @@
 /* End XCBuildConfiguration section */
 
 /* Begin XCConfigurationList section */
-               1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = {
+               1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
                                1DEB928608733DD80010E9CD /* Debug */,

diff --git a/mothur b/mothur
deleted file mode 100755 (executable)
index 2619f5b..0000000
Binary files a/mothur and /dev/null differ