[med-svn] [oases] 03/03: Confirm that relying on the velvet source at build time is not to be solved quickly.
Andreas Tille
tille at debian.org
Wed Dec 13 18:16:15 UTC 2017
This is an automated email from the git hooks/post-receive script.
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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