hisat2: Move pthread control from upstream to pkgsrc

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Jan 13 18:41:59 2019 -0600
Changeset:	6e9c9c1147079a3329d2068014cbfa8170c2e4eb

Modified Files:
	hisat2/Makefile
	hisat2/files/Makefile.pkg

Log Message:
hisat2: Move pthread control from upstream to pkgsrc

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=6e9c9c1147079a3329d2068014cbfa8170c2e4eb

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

diffstat:
 hisat2/Makefile           | 4 +++-
 hisat2/files/Makefile.pkg | 5 +----
 2 files changed, 4 insertions(+), 5 deletions(-)

diffs:
diff --git a/hisat2/Makefile b/hisat2/Makefile
index 16235bcf49..7d87c4dc8e 100644
--- a/hisat2/Makefile
+++ b/hisat2/Makefile
@@ -29,7 +29,9 @@ REPLACE_PERL=		hisat2 scripts/*.sh scripts/*.pl
 REPLACE_PYTHON=		*.py hisat2-build hisat2-inspect
 REPLACE_PYTHON+=	hisatgenotype_modules/*.py hisatgenotype_scripts/*.py
 
-MAKE_FILE=	${FILESDIR}/Makefile.pkg
+MAKE_FILE=		${FILESDIR}/Makefile.pkg
+PTHREAD_AUTO_VARS=	yes
 
 .include "../../lang/python/application.mk"
+.include "../../mk/pthread.buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/hisat2/files/Makefile.pkg b/hisat2/files/Makefile.pkg
index baff77b98c..c70690ac2e 100644
--- a/hisat2/files/Makefile.pkg
+++ b/hisat2/files/Makefile.pkg
@@ -57,9 +57,6 @@ ifeq (1,$(BOWTIE_SHARED_MEM))
 	SHMEM_DEF = -DBOWTIE_SHARED_MEM
 endif
 
-PTHREAD_PKG =
-PTHREAD_LIB = -lpthread
-
 SEARCH_LIBS = 
 BUILD_LIBS = 
 INSPECT_LIBS =
@@ -75,7 +72,7 @@ ifeq (1,$(USE_SRA))
 	SEARCH_LIBS += -L$(NCBI_NGS_DIR)/lib64 -L$(NCBI_VDB_DIR)/lib64
 endif
 
-LIBS = $(PTHREAD_LIB) $(LDFLAGS)
+LIBS = $(LDFLAGS)
 
 SHARED_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
 	edit.cpp gfm.cpp \