From: Michael R. Crusoe <crusoe@debian.org>
Subject: add standard CXXFLAGS CPPFLAGS to Chrysalis & scaffold_iworm_contigs
Forwarded: https://github.com/trinityrnaseq/Chrysalis/pull/1
and https://github.com/trinityrnaseq/trinityrnaseq/pull/1090
--- trinityrnaseq.orig/Chrysalis/Makefile
+++ trinityrnaseq/Chrysalis/Makefile
@@ -1,10 +1,10 @@
 all:
 	mkdir -p build
-	cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install
+	cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && ${MAKE} DESTDIR=../ install
 
 debug:
 	mkdir -p build
-	cd build && cmake -DCMAKE_INSTALL_PREFIX="" -DCMAKE_BUILD_TYPE=Debug ../ && make DESTDIR=../ install
+	cd build && cmake -DCMAKE_INSTALL_PREFIX="" -DCMAKE_BUILD_TYPE=Debug ../ && ${MAKE} DESTDIR=../ install
 
 
 clean:
--- trinityrnaseq.orig/trinity-plugins/scaffold_iworm_contigs/Makefile
+++ trinityrnaseq/trinity-plugins/scaffold_iworm_contigs/Makefile
@@ -2,7 +2,7 @@
 prefix = ../htslib
 
 ScaffoldIwormContigs:
-	$(CXX) $(LDFLAGS) -I$(prefix) -L$(prefix) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs
+	$(CXX) $(LDFLAGS) -I$(prefix) -L$(prefix) $(CPPFLAGS) $(CXXFLAGS) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs
 
 clean:
 	rm -f scaffold_iworm_contigs
