[med-svn] [oases] 03/03: Confirm that relying on the velvet source at build time is not to be solved quickly.

[Andreas Tille]

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tille pushed a commit to branch master
in repository oases.

commit 56bdd63ff3917e8de497c89c69d43ea22f8124de
Author: Andreas Tille <tille at debian.org>
Date:   Wed Dec 13 19:14:45 2017 +0100

    Confirm that relying on the velvet source at build time is not to be solved quickly.
---
 debian/patches/fix-clean-target.patch           |  6 +-
 debian/patches/use-debian-packaged-velvet.patch | 73 +++++++++++++++++++++++--
 2 files changed, 70 insertions(+), 9 deletions(-)

diff --git a/debian/patches/fix-clean-target.patch b/debian/patches/fix-clean-target.patch
index 85f03f1..22f2e5e 100644
--- a/debian/patches/fix-clean-target.patch
+++ b/debian/patches/fix-clean-target.patch
@@ -3,12 +3,12 @@ Subject: Enable flawless cleaning up
 
 --- a/Makefile
 +++ b/Makefile
-@@ -78,7 +78,6 @@ velvetdbg_de :
+@@ -84,7 +84,6 @@ velvetdbg_de :
  
  clean :
  	rm -f obj/*.o obj/dbg/*.o ./oases 
--	cd $(VELVET_DIR) && make clean
- 	cd doc && make clean
+-	make -C $(VELVET_DIR) clean
+ 	make -C doc clean
  
  cleanobj: 
 --- a/doc/manual/Makefile
diff --git a/debian/patches/use-debian-packaged-velvet.patch b/debian/patches/use-debian-packaged-velvet.patch
index c5dbe10..be6bdf5 100644
--- a/debian/patches/use-debian-packaged-velvet.patch
+++ b/debian/patches/use-debian-packaged-velvet.patch
@@ -9,12 +9,73 @@ Subject: Try to use Debian packaged velvet
 
 --- a/Makefile
 +++ b/Makefile
-@@ -29,7 +29,7 @@ ifdef SINGLE_COV_CAT
- override DEF := $(DEF) -D SINGLE_COV_CAT
+@@ -8,7 +8,7 @@ export CATEGORIES = 2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
+ VELVET_DIR=velvet
+ .DEFAULT: default
+-.PHONY: velvet velvetdbg velvet_de velvetdbg_de debug color colordebug
++.PHONY: debug color colordebug
+ 
+ ifdef BIGASSEMBLY
+ override DEF := $(DEF) -D BIGASSEMBLY
+@@ -53,12 +53,6 @@ clean-zlib:
+ 
  endif
  
--default : cleanobj velvet oases doc
-+default : cleanobj oases doc
+-# Velvet dependency
+-VELVET_SRC_DIR=$(VELVET_DIR)/src
+-VELVET_OBJ = recycleBin utility graph passageMarker readSet tightString kmer dfibHeap dfib concatenatedGraph graphStats fibHeap fib readCoherentGraph allocArray binarySequences autoOpen
+-VELVET_FILES = $(VELVET_OBJ:%=$(VELVET_DIR)/obj/%.o)
+-VELVET_DBG_FILES = $(VELVET_OBJ:%=$(VELVET_DIR)/obj/dbg/%.o)
+-
+ # Mac OS users: uncomment the following lines
+ # Z_LIB_FILES=
+ # LDFLAGS = -lm -lz
+@@ -70,35 +64,23 @@ VELVET_DBG_FILES = $(VELVET_OBJ:%=$(VELV
+ OBJ = obj/oases.o obj/transcript.o obj/scaffold.o obj/locallyCorrectedGraph2.o obj/correctedGraph.o obj/filterTranscripts.o obj/locus.o obj/nodeList.o obj/oasesExport.o obj/trivialTranscripts.o obj/complexTranscripts.o obj/extractMergedTranscripts.o obj/extractLoci.o
+ OBJDBG = $(subst obj,obj/dbg,$(OBJ))
+ 
+-velvet :
+-	make -e -C $(VELVET_DIR) obj
+-
+-velvetdbg :
+-	make -e -C $(VELVET_DIR) obj/dbg
+-
+-velvet_de :
+-	make -e -C $(VELVET_DIR) obj_de
+-
+-velvetdbg_de :
+-	make -e -C (VELVET_DIR) obj/dbg_de
+-
+ clean :
+ 	rm -f obj/*.o obj/dbg/*.o ./oases 
+ 	make -C doc clean
+ 
+ cleanobj: 
+-	rm -f obj/*.o obj/dbg/*.o $(VELVET_DIR)/obj/*.o $(VELVET_DIR)/dbg/*.o
++	rm -f obj/*.o obj/dbg/*.o
+ 
+ doc: OasesManual.pdf
+ 
+ OasesManual.pdf: doc/manual/OasesManual.tex
+ 	make -C doc
+ 
+-oases : velvet obj $(OBJ) 
++oases : obj $(OBJ) 
+ 	$(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o oases $(OBJ) $(VELVET_FILES) $(Z_LIB_FILES) $(LIBS)
+ 
+ 
+-debug : cleanobj velvetdbg obj/dbg $(OBJDBG)
++debug : cleanobj obj/dbg $(OBJDBG)
+ 	$(CC) $(CFLAGS) $(DEBUG) $(LDFLAGS) -o oases $(OBJDBG) $(VELVET_DBG_FILES) $(Z_LIB_FILES) $(LIBS)
+ 
+ color : override DEF := $(DEF) -D COLOR
+@@ -116,7 +98,7 @@ obj/dbg:
+ 	mkdir -p obj/dbg
+ 
+ obj/%.o: src/%.c
+-	$(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@ -I$(VELVET_SRC_DIR)
++	$(CC) $(CFLAGS) $(OPT) $(DEF) -c $? -o $@
  
- ifdef BUNDLEDZLIB
- Z_LIB_DIR=$(VELVET_DIR)/third-party/zlib-1.2.3
+ obj/dbg/%.o: src/%.c
+ 	$(CC) $(CFLAGS) $(DEBUG) $(DEF) -c $? -o $@ -I$(VELVET_SRC_DIR)

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