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From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: add standard CXXFLAGS CPPFLAGS to Chrysalis & scaffold_iworm_contigs
--- 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
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