#241

.gitignore

@@ -9,11 +9,13 @@ xcuserdata
 project.xcworkspace
 *.xcuserdata
 TARGET_BUILD_DIRTARGET_BUILD_DIR
+DerivedData
 *.xcuserdata
 *.xml
 nbproject/
 mothur
 Mothur.1
+DerivedData/
 
 *.stdout
 

Makefile

@@ -7,15 +7,23 @@
 #
 # Macros
 #
+# 64BIT_VERSION - set to no if you are using a 32bit arch.
+# OPTIMIZE - yes will increase speed of executable.
+# USEREADLINE - link with readline libraries.  Must have readline installed. Windows set to no.
+# USEBOOST - link with boost libraries. Must install boost. Allows the make.contigs command to read .gz files.
+# BOOST_LIBRARY_DIR - location of boost libraries
+# BOOST_INCLUDE_DIR - location of boost include files
+# MOTHUR_FILES - default location for mothur to look for input files at runtime. Most often used for reference files.
 
 64BIT_VERSION ?= yes
 OPTIMIZE ?= yes
 USEREADLINE ?= yes
 USEBOOST ?= yes
 BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\""
+BOOST_INCLUDE_DIR="\"Enter_your_boost_include_path_here\""
 MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"4/05/2016\""
-VERSION = "\"1.37.0\""
+RELEASE_DATE = "\"3/20/2017\""
+VERSION = "\"1.39.5\""
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
     CXXFLAGS += -DBIT_VERSION
@@ -26,7 +34,8 @@ ifeq  ($(strip $(OPTIMIZE)),yes)
     CXXFLAGS += -O3
 endif
 
-CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION} -O3
+CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION} -std=c++0x
+LDFLAGS += -std=c++0x
 
 ifeq  ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
 else
@@ -44,17 +53,13 @@ ifeq  ($(strip $(USEREADLINE)),yes)
 endif
 
 
-#The boost libraries allow you to read gz files.
+#User specified boost library
 ifeq  ($(strip $(USEBOOST)),yes)
 
-#User specified boost library path
-ifeq  ($(strip $(BOOST_LIBRARY_DIR)),"\"Enter_your_boost_library_path_here\"")
-else
-    LDFLAGS += ${BOOST_LIBRARY_DIR}
-endif
+    LDFLAGS += -L ${BOOST_LIBRARY_DIR}
 
     LIBS += -lboost_iostreams -lz
-    CXXFLAGS += -DUSE_BOOST
+    CXXFLAGS += -DUSE_BOOST -I ${BOOST_INCLUDE_DIR}
 endif
 
 #

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.org/mothur/mothur.svg?branch=v.1.37.0)](https://travis-ci.org/mothur/mothur)
+[![Build Status](https://travis-ci.org/mothur/mothur.svg?branch=master)](https://travis-ci.org/mothur/mothur)
 
 # README