sci-biology/SOAPdenovo2: Respect CC/CXX/CFLAGS/CXXFLAGS variables

This commit cleans up the Makefiles a bit.

1. Do not override user's environment if the variables were are set.

2. Prefer site-wide installation of samtools-0.1.x if existing.

3. Do not force -L/lib or -L/usr/lib64, that is handled by the compiler/linker
   and very importantly, properly.

4. Cleanup spaces and other style inconsistencies.

https://github.com/aquaskyline/SOAPdenovo2/pull/44

Package-Manager: Portage-2.3.31, Repoman-2.3.9

3 files changed, 216 insertions, 9 deletions

diff --git a/sci-biology/SOAPdenovo2/Manifest b/sci-biology/SOAPdenovo2/Manifest
new file mode 100644
index 000000000..047465b7e
--- /dev/null
+++ b/sci-biology/SOAPdenovo2/Manifest
@@ -0,0 +1 @@
+DIST SOAPdenovo2-241.tar.gz 1532760 BLAKE2B 3229ca63b8ecb5012cc8eaa16991ea1385c63da1d7b78c8a3ade6b5fe0b90be08c08d18d3f5e5d708e3af50d5a06e9413807b00e6512965fbc2b8b07ec2dcc6b SHA512 7b0cd992e437f9e5c6f4878c3d3b1fa93f3f8aa3d40895f88cc7a99f7cd69003c4db4d27d7aaa1c2f9f43741f048a74c2479aced44ce4b9432405195749af2e2
diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild
index affce03d3..e3679664d 100644
--- a/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild
+++ b/sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild
@@ -1,14 +1,14 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-inherit toolchain-funcs
+inherit toolchain-funcs eutils
 
 DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph) (now MEGAHIT)"
 HOMEPAGE="https://github.com/aquaskyline/SOAPdenovo2
 	http://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18"
-SRC_URI=""
+SRC_URI="https://github.com/aquaskyline/SOAPdenovo2/archive/r241.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
@@ -19,14 +19,16 @@ DEPEND="dev-libs/libaio
 	sci-biology/samtools:0.1-legacy"
 RDEPEND="${DEPEND}"
 
-S="${WORKDIR}"/"${PN}"-src-r"${PV}" # version is 2.04-r240
+S="${WORKDIR}"/"${PN}"-r"${PV}" # version is 2.04-r241
 
 src_prepare(){
-	# pass to broken Makefile's a proper C++ compiler through the CC variable
-	sed -e "s/CC = g++/CC = "$(tc-getCXX)"/;s/CFLAGS=/CFLAGS = ${CXXFLAGS} #/;s/-lbam/-lbam-0.1-legacy/" -i Makefile || die
-	sed -e 's#-I./sparsePregraph/inc#-I/usr/include/bam-0.1-legacy -I./sparsePregraph/inc#' -i Makefile || die
-	sed -e "s/CC = g++/CC = "$(tc-getCXX)"/;s/CFLAGS=/CFLAGS = ${CXXFLAGS} #/;s/-lbam/-lbam-0.1-legacy/" -i sparsePregraph/Makefile || die
-	sed -e 's#-I./sparsePregraph/inc#-I/usr/include/bam-0.1-legacy -I./sparsePregraph/inc#' -i sparsePregraph/Makefile || die
+	epatch "${FILESDIR}"/SOAPdenovo2-r241-Makefile.patch
+	# this will be partly covered by
+	# https://github.com/aquaskyline/SOAPdenovo2/pull/44
+	#
+	for f in Makefile standardPregraph/Makefile sparsePregraph/Makefile; do
+		sed -e 's#^INCLUDES =#INCLUDES = -I/usr/include/bam-0.1-legacy -I./inc#;s#-lbam#-lbam-0.1-legacy#' -i $f || die
+	done
 	rm -f standardPregraph/*.a standardPregraph/inc/sam.h standardPregraph/inc/bam.h standardPregraph/inc/bgzf.h \
 		sparsePregraph/inc/sam.h sparsePregraph/inc/bam.h sparsePregraph/inc/bgzf.h standardPregraph/inc/zlib.h \
 		standardPregraph/inc/zconf.h sparsePregraph/inc/zlib.h sparsePregraph/inc/zconf.h standardPregraph/inc/*.so \
diff --git a/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch b/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch
new file mode 100644
index 000000000..a710c2d86
--- /dev/null
+++ b/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch
@@ -0,0 +1,204 @@
+--- sparsePregraph/Makefile.ori	2017-01-03 21:34:59.000000000 +0100
++++ sparsePregraph/Makefile	2018-04-22 22:07:47.303546845 +0200
+@@ -1,28 +1,28 @@
+-CC=            g++
++CXX ?= g++
+ ifdef debug
+-CFLAGS=         -O0 -g -fomit-frame-pointer
++CXXFLAGS ?= -O0 -g -fomit-frame-pointer
+ else
+-CFLAGS=         -O3 -fomit-frame-pointer -w
++CXXFLAGS ?= -O3 -fomit-frame-pointer -w
+ endif
+ 
+-DFLAGS=         
+-OBJS=		build_graph.o build_edge.o multi_threads.o \
+-			build_preArc.o pregraph_sparse.o io_func.o\
+-			global.o convert_soapdenovo.o
+-PROG=           
+-INCLUDES=	-I./inc
+-SUBDIRS=    . 
+-LIBPATH=	-L/usr/lib64
+-LIBS=       -pthread -lz -L./inc
++DFLAGS =         
++OBJS = build_graph.o build_edge.o multi_threads.o \
++	build_preArc.o pregraph_sparse.o io_func.o\
++	global.o convert_soapdenovo.o
++PROG =           
++INCLUDES = -I./inc
++SUBDIRS = . 
++LIBPATH = -L/usr/lib64
++LIBS = -pthread -lz -L./inc
+ EXTRA_FLAGS=
+-VERSION =    1.0.3
++VERSION = 1.0.3
+ 
+ ifdef 127mer
+-CFLAGS += -D_127MER_
++CXXFLAGS += -D_127MER_
+ PROG = pregraph_sparse_127mer.v$(VERSION)
+ 
+ else
+-CFLAGS += -D_63MER_
++CXXFLAGS += -D_63MER_
+ PROG = pregraph_sparse_63mer.v$(VERSION)
+ endif
+ 
+@@ -38,22 +38,22 @@
+ endif
+ 
+ ifneq (,$(findstring $(shell uname -m), x86_64))
+-CFLAGS += -m64
++CXXFLAGS += -m64
+ endif
+ 
+ ifneq (,$(findstring $(shell uname -m), ia64))
+-CFLAGS += 
++CXXFLAGS += 
+ endif
+ 
+ ifneq (,$(findstring $(shell uname -m), ppc64))
+-CFLAGS += -mpowerpc64
++CXXFLAGS += -mpowerpc64
+ endif
+ 
+ .SUFFIXES:.cpp .o
+ 
+ .cpp.o:
+ 		@printf "Compiling $<...                               \r"
+-		@$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<"
++		@$(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $<"
+ 
+ all:		$(OBJS) 
+ 		@printf "$(PROG) objects generated.                    \n"
+@@ -66,7 +66,7 @@
+ 
+ pregraph_sparse: clean envTest $(OBJS)
+ 		@printf "Linking...                                     \r"
+-		@$(CC) $(CFLAGS)$(INCLUDES) -o $(PROG)  $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
++		@$(CXX) $(CXXFLAGS)$(INCLUDES) -o $(PROG)  $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
+ 		@printf "$(PROG) compilation done.                      \n"
+ 
+ clean:
+--- Makefile.ori	2017-01-03 21:34:59.000000000 +0100
++++ Makefile	2018-04-22 22:09:16.526124921 +0200
+@@ -1,17 +1,17 @@
+ MAKEFLAGS += --no-print-directory
+-CC = g++
++CXX ?= g++
+ ifdef debug
+-CFLAGS=         -O0 -g -fomit-frame-pointer
++CXXFLAGS ?= -O0 -g -fomit-frame-pointer
+ else
+-CFLAGS=         -O3 -fomit-frame-pointer
++CXXFLAGS ?= -O3 -fomit-frame-pointer
+ endif
+ 
+ SUBDIRS = sparsePregraph standardPregraph fusion
+-PROG=       SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion
+-INCLUDES=   -I./sparsePregraph/inc -I./standardPregraph/inc
++PROG = SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion
++INCLUDES = -I./sparsePregraph/inc -I./standardPregraph/inc
+ 
+-LIBPATH=    -L/lib64 -L/usr/lib64 -L./sparsePregraph/inc -L./standardPregraph/inc
+-LIBS=       -pthread -lz -lm
++LIBPATH = -L./sparsePregraph/inc -L./standardPregraph/inc
++LIBS = -pthread -lz -lm
+ EXTRA_FLAGS= 
+ 
+ BIT_ERR = 0
+@@ -25,15 +25,15 @@
+ endif
+ 
+ ifneq (,$(findstring $(shell uname -m), x86_64))
+-CFLAGS += -m64
++CXXFLAGS += -m64
+ endif
+ 
+ ifneq (,$(findstring $(shell uname -m), ia64))
+-CFLAGS +=
++CXXFLAGS +=
+ endif
+ 
+ ifneq (,$(findstring $(shell uname -m), ppc64))
+-CFLAGS += -mpowerpc64
++CXXFLAGS += -mpowerpc64
+ endif
+ 
+ 
+@@ -46,20 +46,20 @@
+ SOAPdenovo-63mer:
+ 	@cd sparsePregraph;make 63mer=1 debug=1;cd ..;
+ 	@cd standardPregraph;make 63mer=1 debug=1;cd ..;
+-	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
++	@$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
+ SOAPdenovo-127mer:
+ 	@cd sparsePregraph;make 127mer=1 debug=1;cd ..;
+ 	@cd standardPregraph;make 127mer=1 debug=1;cd ..;
+-	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
++	@$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
+ else
+ SOAPdenovo-63mer:
+ 	@cd sparsePregraph;make 63mer=1;cd ..;
+ 	@cd standardPregraph;make 63mer=1;cd ..;
+-	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
++	@$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
+ SOAPdenovo-127mer:
+ 	@cd sparsePregraph;make 127mer=1;cd ..;
+ 	@cd standardPregraph;make 127mer=1;cd ..;
+-	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
++	@$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
+ endif
+ 
+ clean:
+--- standardPregraph/Makefile.ori	2017-01-03 21:34:59.000000000 +0100
++++ standardPregraph/Makefile	2018-04-22 22:10:33.108337752 +0200
+@@ -5,13 +5,13 @@
+ #
+ ###################################
+ 
+-CC=             gcc
++CC ?= gcc
+ GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4)
+ GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4)
+ ifdef debug
+-CFLAGS=         -O0 -g -fomit-frame-pointer #-msse4.2
++CFLAGS ?= -O0 -g -fomit-frame-pointer #-msse4.2
+ else
+-CFLAGS=         -O3 -fomit-frame-pointer -w #-msse4.2
++CFLAGS ?= -O3 -fomit-frame-pointer -w #-msse4.2
+ endif
+ DFLAGS=         
+ OBJS=		arc.o attachPEinfo.o bubble.o check.o compactEdge.o \
+@@ -24,12 +24,12 @@
+ 		prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o\
+ 		readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o \
+ 		cutTip_graph2.o linearEdge.o kmerhash.o read2edge.o iterate.o
+-PROG=       SOAPdenovo-63mer
+-INCLUDES=   -Iinc
+-SUBDIRS=    .
+-LIBPATH=    -L/lib64 -L/usr/lib64 -L./inc
+-LIBS=       -pthread -lz -lm 
+-EXTRA_FLAGS=
++PROG = SOAPdenovo-63mer
++INCLUDES = -Iinc
++SUBDIRS = .
++LIBPATH = -L./inc
++LIBS = -pthread -lz -lm 
++EXTRA_FLAGS =
+ 
+ BIT_ERR = 0
+ ifeq (,$(findstring $(shell uname -m), x86_64 ppc64 ia64))
+--- fusion/Makefile.ori	2017-01-03 21:34:59.000000000 +0100
++++ fusion/Makefile	2018-04-22 22:11:21.209727636 +0200
+@@ -6,8 +6,8 @@
+ libdir = 
+ mandir = 
+ 
+-CC = gcc
+-CCOPT = -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w 
++CC ?= gcc
++CCOPT ?= -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w 
+ LIBS = -lm -lpthread
+ INCDIRS = -Iinc/
+ CFLAGS = ${CCOPT} ${INCDIRS}