--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/package/Makefile	Tue Jan 20 16:23:33 2015 -0500
@@ -0,0 +1,58 @@
+DEBUG ?= 0
+PARALLEL ?= 0
+
+# External Libraries
+BOOST_ROOT ?= /g/solexa/bin/software/boost_1_53_0/
+BAMTOOLS_ROOT ?= /g/solexa/bin/software/bamtools-2.3.0/
+SEQTK_ROOT ?= /g/solexa/bin/software/kseq/
+
+# Flags
+CXX=g++
+CXXFLAGS += -isystem ${BOOST_ROOT}/include -isystem ${BAMTOOLS_ROOT}/include -isystem ${SEQTK_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas
+LDFLAGS += -L${BOOST_ROOT}/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -L${BAMTOOLS_ROOT}/lib -lbamtools -lz -Wl,-rpath,${BAMTOOLS_ROOT}/lib,-rpath,${BOOST_ROOT}/lib
+
+# Additional flags for release/debug
+ifeq (${PARALLEL}, 1)
+	CXXFLAGS += -fopenmp -DOPENMP
+else
+	CXXFLAGS += -DNOPENMP
+endif
+
+# Additional flags for release/debug
+ifeq (${DEBUG}, 1)
+	CXXFLAGS += -g -O0 -fno-inline -DDEBUG
+else ifeq (${DEBUG}, 2)
+	CXXFLAGS += -g -O0 -fno-inline -DPROFILE
+	LDFLAGS += -lprofiler -ltcmalloc
+else
+	CXXFLAGS += -O9 -DNDEBUG
+	#LDFLAGS += --static
+endif
+
+# External sources
+HTSLIBSOURCES = $(wildcard src/htslib/*.c) $(wildcard src/htslib/*.h)
+BAMTOOLSSOURCES = $(wildcard src/bamtools/src/api/*.h) $(wildcard src/bamtools/src/api/*.cpp)
+DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp)
+
+# Targets
+TARGETS = src/delly src/extract src/cov src/iover src/stats
+
+all: $(TARGETS)
+
+src/delly: $(DELLYSOURCES)
+	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
+
+src/extract: $(DELLYSOURCES)
+	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
+
+src/cov: $(DELLYSOURCES)
+	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
+
+src/iover: $(DELLYSOURCES)
+	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
+
+src/stats: $(DELLYSOURCES)
+	$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
+
+clean:
+	rm -f $(TARGETS) $(TARGETS:=.o) 

--- a/package/tool_dependencies.xml	Tue Jan 20 15:09:34 2015 -0500
+++ b/package/tool_dependencies.xml	Tue Jan 20 16:23:33 2015 -0500
@@ -17,9 +17,9 @@
 			<install version="1.0">
 				<actions>
 					<action type="download_by_url">https://github.com/tobiasrausch/delly/archive/v0.6.1.tar.gz</action>
-					<action type="download_by_url">https://raw.githubusercontent.com/morinlab/galaxy_tools/master/delly/Makefile?token=AKBWDhpiQthVaz3plMQkg4ACAPGEQK1Wks5Ux-25wA%3D%3D</action>
+					<action type="shell_command">ls $REPOSITORY_INSTALL_DIR</action>
 					<action type="move_directory_files">
-						<source_directory>./Makefile?token*</source_directory>
+						<source_directory>$REPOSITORY_INSTALL_DIR/Makefile</source_directory>
 						<destination_directory>./Makefile</destination_directory>
 					</action>
 					<action type="shell_command">make all BOOST_ROOT=\$BOOST_ROOT BAMTOOLS_ROOT=\$BAMTOOLS_ROOT SEQTK_ROOT=\$SEQTK_ROOT</action>