freebayes: Make submodule makefiles respect LDFLAGS and find zlib

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Sat Mar 31 09:02:08 2018 -0500
Changeset:	42d2a01c3a2b0f1a1fae47697fed404484d3f814

Modified Files:
	ddocent/Makefile
	freebayes/Makefile
	freebayes/distinfo
	freebayes/patches/patch-SeqLib_bwa_Makefile
	freebayes/patches/patch-SeqLib_fermi-lite_Makefile
Added Files:
	freebayes/patches/patch-vcflib_tabixpp_Makefile

Log Message:
freebayes: Make submodule makefiles respect LDFLAGS and find zlib

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=42d2a01c3a2b0f1a1fae47697fed404484d3f814

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 ddocent/Makefile                                   |  3 +--
 freebayes/Makefile                                 |  8 ++++----
 freebayes/distinfo                                 |  5 +++--
 freebayes/patches/patch-SeqLib_bwa_Makefile        | 18 ++++++++++++++++--
 freebayes/patches/patch-SeqLib_fermi-lite_Makefile | 14 ++++++++++++--
 freebayes/patches/patch-vcflib_tabixpp_Makefile    | 15 +++++++++++++++
 6 files changed, 51 insertions(+), 12 deletions(-)

diffs:
diff --git a/ddocent/Makefile b/ddocent/Makefile
index eef2b69e08..7d9c608618 100644
--- a/ddocent/Makefile
+++ b/ddocent/Makefile
@@ -35,8 +35,7 @@ DEPENDS=	mawk>=0:../../lang/mawk \
 		seqtk>=0:../../wip/seqtk \
 		bedtools2>=2.26.0:../../wip/bedtools2 \
 		pear-merger>=0:../../wip/pear-merger \
-
-#		freebayes>=0:../../wip/freebayes
+		freebayes>=0:../../wip/freebayes
 
 ## These follow patch-dDocent, so don't apply them within the source tree,
 ## or they'll get picked up by patch generators and hard-code PREFIX
diff --git a/freebayes/Makefile b/freebayes/Makefile
index e024afe3fe..c9b5293446 100644
--- a/freebayes/Makefile
+++ b/freebayes/Makefile
@@ -17,10 +17,10 @@ USE_TOOLS+=	gmake
 
 MAKE_JOBS_SAFE=	no
 
-SUBST_CLASSES+=           compile
-SUBST_FILES.compile=      ${WRKSRC}/src/Makefile.external-libs
-SUBST_STAGE.compile=      post-patch
-SUBST_SED.compile+=       -e "s|-lm|-lm ${COMPILER_RPATH_FLAG}${PREFIX}/lib|g"
+#SUBST_CLASSES+=           compile
+#SUBST_FILES.compile=      ${WRKSRC}/src/Makefile.external-libs
+#SUBST_STAGE.compile=      post-patch
+#SUBST_SED.compile+=       -e "s|-lm|-lm ${COMPILER_RPATH_FLAG}${PREFIX}/lib|g"
 
 .include "../../mk/bsd.prefs.mk"
 
diff --git a/freebayes/distinfo b/freebayes/distinfo
index 1aa6d4a556..1cbac2cfc1 100644
--- a/freebayes/distinfo
+++ b/freebayes/distinfo
@@ -5,12 +5,13 @@ RMD160 (freebayes-2018.03.23.tar.xz) = bde7a441c76c2a16c89600d8b3fe0ce843146b37
 SHA512 (freebayes-2018.03.23.tar.xz) = 04f386b24d623e4b818a2b3ce12042c30db877b9ab08744466702573730ff8f853f7f2720d9a23f3c7b3abae8dc50fba3912e1695ad7d04dbddc3682754952e4
 Size (freebayes-2018.03.23.tar.xz) = 89782932 bytes
 SHA1 (patch-Makefile) = aace859fb9e85a132386d510771c34f0b9a0d47b
-SHA1 (patch-SeqLib_bwa_Makefile) = 2822b4c3c8c612033fba165d918a790711e28bba
+SHA1 (patch-SeqLib_bwa_Makefile) = 3f8c8bd8720d5a4ceb7e29d1b83eba285d038323
 SHA1 (patch-SeqLib_bwa_bwt__lite.c) = de4f9efd1485a4b6c20837584e65406267833ccd
 SHA1 (patch-SeqLib_bwa_bwtgap.h) = a8abe98b7f0ad65104a763c19fd128bbb05f2ed8
 SHA1 (patch-SeqLib_bwa_kthread.c) = 5170b400af2f1f835cfcf5dda3875242f227bc89
-SHA1 (patch-SeqLib_fermi-lite_Makefile) = 1f1d19792bcfca7cf76076243e2e0ee218e53e4a
+SHA1 (patch-SeqLib_fermi-lite_Makefile) = 55d999277d5d61dba7cae01b44a8f9ebff77142d
 SHA1 (patch-SeqLib_htslib_Makefile) = f7d332c3defd580a44feaa479e5c17509f73e02d
 SHA1 (patch-src_LargeFileSupport.h) = 2efb9a247582c85b080a1e1346e687c99686749d
 SHA1 (patch-src_Makefile) = afd89cc38dd7cd94d0d4a698a54a1c2a6be87f29
 SHA1 (patch-vcflib_Makefile) = ce29ade87027b7e638f0472653cec6e9aa809b15
+SHA1 (patch-vcflib_tabixpp_Makefile) = 433ddd3e4e643376fd0f7511032d6d20ab676459
diff --git a/freebayes/patches/patch-SeqLib_bwa_Makefile b/freebayes/patches/patch-SeqLib_bwa_Makefile
index a471484c89..21f989ed87 100644
--- a/freebayes/patches/patch-SeqLib_bwa_Makefile
+++ b/freebayes/patches/patch-SeqLib_bwa_Makefile
@@ -1,7 +1,8 @@
 $NetBSD$
 
-Allow makefile variable overrides.
---- SeqLib/bwa/Makefile.orig	2018-03-23 18:47:04 UTC
+# Respect LDFLAGS from pkgsrc
+
+--- SeqLib/bwa/Makefile.orig	2018-03-23 14:01:29.000000000 +0000
 +++ SeqLib/bwa/Makefile
 @@ -1,8 +1,8 @@
 -CC=			gcc
@@ -15,3 +16,16 @@ Allow makefile variable overrides.
  DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
  ## moved is.o bwtiindex.o rope.o to LOBJS
  LOBJS=		utils.o kthread.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o \
+@@ -28,10 +28,10 @@ endif
+ all:$(PROG)
+ 
+ bwa:libbwa.a $(AOBJS) main.o
+-		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
++	$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. $(LDFLAGS) -lbwa $(LIBS)
+ 
+ bwamem-lite:libbwa.a example.o
+-		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
++	$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. $(LDFLAGS) -lbwa $(LIBS)
+ 
+ libbwa.a:$(LOBJS)
+ 		$(AR) -csru $@ $(LOBJS)
diff --git a/freebayes/patches/patch-SeqLib_fermi-lite_Makefile b/freebayes/patches/patch-SeqLib_fermi-lite_Makefile
index c7b746bb9b..1a802a4aa3 100644
--- a/freebayes/patches/patch-SeqLib_fermi-lite_Makefile
+++ b/freebayes/patches/patch-SeqLib_fermi-lite_Makefile
@@ -1,7 +1,8 @@
 $NetBSD$
 
-Allow makefile variable overrides.
---- SeqLib/fermi-lite/Makefile.orig	2018-03-23 18:50:25 UTC
+# Respect LDFLAGS from pkgsrc
+
+--- SeqLib/fermi-lite/Makefile.orig	2018-03-23 14:01:29.000000000 +0000
 +++ SeqLib/fermi-lite/Makefile
 @@ -1,6 +1,6 @@
 -CC=			gcc
@@ -13,3 +14,12 @@ Allow makefile variable overrides.
  INCLUDES=	
  OBJS=		kthread.o misc.o \
  			bseq.o htab.o bfc.o \
+@@ -17,7 +17,7 @@ LIBS=		-lm -lz -lpthread
+ all:$(PROG)
+ 
+ fml-asm:libfml.a example.o
+-		$(CC) $(CFLAGS) $^ -o $@ -L. -lfml $(LIBS)
++		$(CC) $(CFLAGS) $^ -o $@ -L. $(LDFLAGS) -lfml $(LIBS)
+ 
+ libfml.a:$(OBJS)
+ 		$(AR) -csru $@ $(OBJS)
diff --git a/freebayes/patches/patch-vcflib_tabixpp_Makefile b/freebayes/patches/patch-vcflib_tabixpp_Makefile
new file mode 100644
index 0000000000..ee18552345
--- /dev/null
+++ b/freebayes/patches/patch-vcflib_tabixpp_Makefile
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Respect LDFLAGS from pkgsrc
+
+--- vcflib/tabixpp/Makefile.orig	2018-03-31 13:42:56.711911472 +0000
++++ vcflib/tabixpp/Makefile
+@@ -39,7 +39,7 @@ htslib/libhts.a:
+ 
+ tabix++: tabix.o main.cpp $(HTS_LIB)
+ 	$(CXX) $(CXXFLAGS) -o $@ main.cpp tabix.o $(INCLUDES) $(LIBPATH) \
+-		-lhts -lpthread -lm -lz
++		$(LDFLAGS) -lhts -lpthread -lm -lz
+ 
+ cleanlocal:
+ 	rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a tabix.aux tabix.log \