Changes to some Makefiles so that the code can be built from the root…

… of the dir tree

Makefile

@@ -0,0 +1,36 @@
+#    This file is part of the methpipe system
+#
+#    Copyright (C) 2014 University of Southern California,
+#                       Andrew D. Smith
+#
+#    Authors: Andrew D. Smith
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+AMORDAD_ROOT := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
+
+all:
+	@make -C src AMORDAD_ROOT=$(AMORDAD_ROOT) OPT=1
+
+install:
+	@make -C src AMORDAD_ROOT=$(AMORDAD_ROOT) OPT=1 install
+
+clean:
+	@make -C src AMORDAD_ROOT=$(AMORDAD_ROOT) clean
+.PHONY: clean
+
+distclean: clean
+	@rm -rf $(AMORDAD_ROOT)/bin
+.PHONY: distclean

src/Makefile

@@ -0,0 +1,50 @@
+#    This file is part of the methpipe system
+#
+#    Copyright (C) 2014 University of Southern California,
+#                       Andrew D. Smith
+#
+#    Authors: Andrew D. Smith
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+all_subdirs=common progs
+lib_subdirs=common
+app_subdirs=progs
+
+# check if a global copy of smithlab_cpp cannot be found and try to
+# use a copy that is in the current directory
+ifndef SMITHLAB_CPP
+	SMITHLAB_CPP=$(abspath $(dir $(MAKEFILE_LIST)))/smithlab_cpp
+	ifeq ("$(wildcard $(SMITHLAB_CPP))","")
+		$(error SMITHLAB_CPP not set and smithlab_cpp not found)
+	endif
+	all_subdirs += $(SMITHLAB_CPP)
+	lib_subdirs += $(SMITHLAB_CPP)
+endif
+
+all:
+	@for i in $(app_subdirs); do \
+		make -C $${i} SMITHLAB_CPP=$(SMITHLAB_CPP) OPT=1; \
+	done;
+
+install:
+	@for i in $(app_subdirs); do \
+		make -C $${i} SMITHLAB_CPP=$(SMITHLAB_CPP) OPT=1 install; \
+	done;
+
+clean:
+	@for i in $(all_subdirs); do \
+		make -C $${i} SMITHLAB_CPP=$(SMITHLAB_CPP) clean; \
+	done;

src/progs/Makefile

@@ -23,7 +23,10 @@ PROGS = build_graph_naively naive_batch_query \
 	amordad_batch_query \
 	simulate_feature_vector
 
-SMITHLAB_CPP = ../smithlab_cpp
+ifndef SMITHLAB_CPP
+	SMITHLAB_CPP = ../smithlab_cpp
+endif
+
 COMMON = ../common
 
 INCLUDEDIRS = $(SMITHLAB_CPP) $(COMMON)