diff --git a/Makefile b/Makefile
index e54786d..ea03564 100644
--- a/Makefile
+++ b/Makefile
@@ -1,5 +1,5 @@
 
-virtPyDir = $(CURDIR)/python
+virtPyDir = $(PWD)/python
 virtPyEnv = ${virtPyDir}/bin/activate
 virtPy = ${virtPyDir}/bin/python
 export
diff --git a/submodules/Makefile b/submodules/Makefile
index 07fc371..db56cfe 100644
--- a/submodules/Makefile
+++ b/submodules/Makefile
@@ -16,20 +16,20 @@ envRefreshRule:
 	rm -f ${myEnv}
 
 virtPyRule :
-	python $(CURDIR)/virtualenv/virtualenv.py ${virtPyDir}
-	. ${virtPyEnv} && cd $(CURDIR)/networkx && ${virtPy} setup.py install
-	. ${virtPyEnv} && cd $(CURDIR)/psutil/ && ${virtPy} setup.py install
+	python $(PWD)/virtualenv/virtualenv.py ${virtPyDir}
+	. ${virtPyEnv} && cd $(PWD)/networkx && ${virtPy} setup.py install
+	. ${virtPyEnv} && cd $(PWD)/psutil/ && ${virtPy} setup.py install
 	cp ${virtPyEnv} ${myEnv}
-	echo export PYTHONPATH=$(CURDIR):\$$PYTHONPATH >> ${myEnv}
+	echo export PYTHONPATH=$(PWD):\$$PYTHONPATH >> ${myEnv}
 	echo export PATH=${virtPyDir}/bin:\$$PATH >> ${myEnv}
 
 ifeq ($(enablePBSTorque), yes)
 pbsDrmaaRule :
-	cd pbs-drmaa &&./configure --prefix=$(CURDIR)/pbs-drmaa && make && make install
-	echo export DRMAA_LIBRARY_PATH=$(CURDIR)/pbs-drmaa/lib/libdrmaa.so >> ${myEnv}
+	cd pbs-drmaa &&./configure --prefix=$(PWD)/pbs-drmaa && make && make install
+	echo export DRMAA_LIBRARY_PATH=$(PWD)/pbs-drmaa/lib/libdrmaa.so >> ${myEnv}
 
 drmaaPythonRule :
-	. ${virtPyEnv} && cd $(CURDIR)/drmaa-python/ && ${virtPy} setup.py install
+	. ${virtPyEnv} && cd $(PWD)/drmaa-python/ && ${virtPy} setup.py install
 else
 pbsDrmaaRule :
 	cd .
@@ -39,24 +39,24 @@ drmaaPythonRule :
 endif
 
 zlibRule :
-	cd zlib && ./configure --prefix=$(CURDIR)/zlib && make && make install
-	echo export PATH=$(CURDIR)/zlib/bin:\$$PATH >> ${myEnv}
+	cd zlib && ./configure --prefix=$(PWD)/zlib && make && make install
+	echo export PATH=$(PWD)/zlib/bin:\$$PATH >> ${myEnv}
 
 tokyocabinetRule :
-	cd tokyocabinet &&./configure --prefix=$(CURDIR)/tokyocabinet ${ktlinkingflags} --disable-bzip && make && make install
-	echo export PATH=$(CURDIR)/tokyocabinet/bin:\$$PATH >> ${myEnv}
+	cd tokyocabinet &&./configure --prefix=$(PWD)/tokyocabinet ${ktlinkingflags} --disable-bzip && make && make install
+	echo export PATH=$(PWD)/tokyocabinet/bin:\$$PATH >> ${myEnv}
 
 kyotocabinetRule :
-	cd kyotocabinet &&./configure --prefix=$(CURDIR)/kyotocabinet ${ktlinkingflags} && make && make install
-	echo export PATH=$(CURDIR)/kyotocabinet/bin:\$$PATH >> ${myEnv}
+	cd kyotocabinet &&./configure --prefix=$(PWD)/kyotocabinet ${ktlinkingflags} && make && make install
+	echo export PATH=$(PWD)/kyotocabinet/bin:\$$PATH >> ${myEnv}
 
 kyototycoonRule :
-	cd kyototycoon &&./configure --prefix=$(CURDIR)/kyototycoon ${ktlinkingflags} --with-kc=$(CURDIR)/kyotocabinet && make && make install
+	cd kyototycoon &&./configure --prefix=$(PWD)/kyototycoon ${ktlinkingflags} --with-kc=$(PWD)/kyotocabinet && make && make install
 	echo export LD_LIBRARY_PATH=$(LD_LIBRARY_PATH) >> ${myEnv}
-	echo export PATH=$(CURDIR)/kyototycoon/bin:\$$PATH >> ${myEnv}
+	echo export PATH=$(PWD)/kyototycoon/bin:\$$PATH >> ${myEnv}
 
 ifneq ($(TARGETOS), Darwin)
-CLAPACKPHASTFLAGS = CLAPACKPATH=$(CURDIR)/clapack
+CLAPACKPHASTFLAGS = CLAPACKPATH=$(PWD)/clapack
 clapackRule :
 	cd clapack && make f2clib && make blaslib && make lib
 else
@@ -68,7 +68,7 @@ endif
 ifdef ENABLE_PHYLOP
 phastRule :
 	cd phast/src && make $(CLAPACKPHASTFLAGS)
-	echo export PATH=$(CURDIR)/phast/bin:\$$PATH >> ${myEnv}
+	echo export PATH=$(PWD)/phast/bin:\$$PATH >> ${myEnv}
 else
 phastRule :
 	cd .
@@ -76,11 +76,11 @@ endif
 
 kentToolBinariesRule :
 	cd kentToolBinaries && make
-	echo export PATH=$(CURDIR)/kentToolBinaries:\$$PATH >> ${myEnv}
+	echo export PATH=$(PWD)/kentToolBinaries:\$$PATH >> ${myEnv}
 
 hdf5Rule :
-	cd hdf5 &&./configure --prefix=$(CURDIR)/hdf5 --enable-cxx && make && make install
-	echo export PATH=$(CURDIR)/hdf5/bin:\$$PATH >> ${myEnv}
+	cd hdf5 &&./configure --prefix=$(PWD)/hdf5 --enable-cxx && make && make install
+	echo export PATH=$(PWD)/hdf5/bin:\$$PATH >> ${myEnv}
 
 
 # Important to export environment to override sonlib/include.mk
@@ -88,7 +88,7 @@ export
 
 ucsc.%:
 	cd $* && make
-	echo export PATH=$(CURDIR)/$*/bin:\$$PATH >> ${myEnv}
+	echo export PATH=$(PWD)/$*/bin:\$$PATH >> ${myEnv}
 
 clean: cabinetClean hdf5Clean pbsDrmaaClean zlibClean clapackClean phastClean kentToolBinariesClean ${ucscModules:%=clean.%}
 
@@ -106,7 +106,7 @@ zlibClean:
 cabinetClean:
 	cd kyotocabinet && make clean
 	cd kyototycoon && make clean
-	rm -f $(CURDIR)/tokyocabinet/lib/*.a $(CURDIR)/kyotocabinet/lib/*.a  $(CURDIR)/kyototycoon/lib/*.a
+	rm -f $(PWD)/tokyocabinet/lib/*.a $(PWD)/kyotocabinet/lib/*.a  $(PWD)/kyototycoon/lib/*.a
 
 ifeq ($(enablePBSTorque), yes)
 pbsDrmaaClean:
@@ -144,4 +144,4 @@ test.%:
 	. ${myEnv} && cd $* && make test
 
 datasets:
-	echo export SON_TRACE_DATASETS=$(CURDIR)/cactusTestData >> ${myEnv}
+	echo export SON_TRACE_DATASETS=$(PWD)/cactusTestData >> ${myEnv}
diff --git a/submodules/include.mk b/submodules/include.mk
index 4c93ed9..8ccc0dc 100644
--- a/submodules/include.mk
+++ b/submodules/include.mk
@@ -1,17 +1,17 @@
 #Modify this variable to set the location of sonLib
-sonLibRootPath=$(CURDIR)/sonLib
+sonLibRootPath=$(PWD)/sonLib
 sonLibPath=${sonLibRootPath}/lib
 
 
 #OVERRIDE SONLIB WITH LOCAL DBS (because now sonlib won't redefine if exist)
-tcPrefix = $(CURDIR)/tokyocabinet
+tcPrefix = $(PWD)/tokyocabinet
 tokyoCabinetIncl = -I ${tcPrefix}/include -DHAVE_TOKYO_CABINET=1
 tokyoCabinetLib = -L${tcPrefix}/lib -Wl,-rpath,${tcPrefix}/lib -ltokyocabinet -lz -lpthread -lm
 
-kcPrefix =$(CURDIR)/kyotocabinet
-ttPrefix =$(CURDIR)/kyototycoon
-kyotoTycoonIncl = -I${kcPrefix}/include -I${ttPrefix}/include -DHAVE_KYOTO_TYCOON=1 -I$(CURDIR)/zlib/include 
-kyotoTycoonLib = -L$(CURDIR)/zlib/lib -L${ttPrefix}/lib -Wl,-rpath,${ttPrefix}/lib -lkyototycoon -L${kcPrefix}/lib -Wl,-rpath,${kcPrefix}/lib -lkyotocabinet -Wl,-rpath,$(CURDIR)/zlib/lib -lz -lpthread -lm -lstdc++
+kcPrefix =$(PWD)/kyotocabinet
+ttPrefix =$(PWD)/kyototycoon
+kyotoTycoonIncl = -I${kcPrefix}/include -I${ttPrefix}/include -DHAVE_KYOTO_TYCOON=1 -I$(PWD)/zlib/include 
+kyotoTycoonLib = -L$(PWD)/zlib/lib -L${ttPrefix}/lib -Wl,-rpath,${ttPrefix}/lib -lkyototycoon -L${kcPrefix}/lib -Wl,-rpath,${kcPrefix}/lib -lkyotocabinet -Wl,-rpath,$(PWD)/zlib/lib -lz -lpthread -lm -lstdc++
 
 #DISABLE MYSQUL
 mysqlIncl = 
@@ -29,18 +29,18 @@ basicLibs = ${sonLibPath}/sonLib.a ${sonLibPath}/cuTest.a ${dblibs}
 basicLibsDependencies = ${sonLibPath}/sonLib.a ${sonLibPath}/cuTest.a 
 
 #put hdf5 at beginning of path
-h5path = $(CURDIR)/hdf5
+h5path = $(PWD)/hdf5
 PATH := ${h5path}/bin:${PATH}
 h5prefix = -prefix=${h5path}
 
 #environment
-myEnv = $(CURDIR)/../environment
+myEnv = $(PWD)/../environment
 
 #kyoto tycoon et al have problems with shared libraries on the cluster
 #but shared libraries seem to be necessary to build on osx.
-LDFLAGS := -L$(CURDIR)/zlib/lib -L$(CURDIR)/kyotocabinet/lib $(LDFLAGS)
+LDFLAGS := -L$(PWD)/zlib/lib -L$(PWD)/kyotocabinet/lib $(LDFLAGS)
 CXXFLAGS := $(cppflags) $(CXXFLAGS)
-LD_LIBRARY_PATH := $(CURDIR)/zlib/lib:$(CURDIR)/kyotocabinet/lib:$(CURDIR)/kyototycoon/lib:$(LD_LIBRARY_PATH)
+LD_LIBRARY_PATH := $(PWD)/zlib/lib:$(PWD)/kyotocabinet/lib:$(PWD)/kyototycoon/lib:$(LD_LIBRARY_PATH)
 #UNAME := $(shell uname)
 #ifeq ($(UNAME), Darwin)
 ktlinkingflags =