biology/bcftools: update to 1.9

While here:

* Update LICENSE handling
* Move all commands to bin/

PR:	230169
Submitted by:	ndowens.fbsd@yandex.com
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D16543

5 files changed, 41 insertions, 24 deletions

diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile
index 72b06e4e09b6..c9cac440562f 100644
--- a/biology/bcftools/Makefile
+++ b/biology/bcftools/Makefile
@@ -2,15 +2,14 @@
 # $FreeBSD$
 
 PORTNAME=	bcftools
-PORTVERSION=	1.6
-PORTREVISION=	1
+PORTVERSION=	1.9
 CATEGORIES=	biology
 
 MAINTAINER=	cartwright@asu.edu
 COMMENT=	Tools for manipulating next-generation sequencing data
 
 LICENSE=	MIT
-# LICENSE_FILE=	${WRKSRC}/LICENSE
+LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	htslib>=1.6:biology/htslib
 LIB_DEPENDS=	libhts.so:biology/htslib
@@ -18,13 +17,15 @@ TEST_DEPENDS=	bash:shells/bash
 
 CONFLICTS_BUILD=openssl
 
+USES=		autoreconf gmake localbase \
+		perl5 python:env shebangfix
+
 USE_GITHUB=	yes
 GH_ACCOUNT=	samtools
 
-USES=		autoreconf gmake perl5 python:env shebangfix
+USE_LDCONFIG=	${PREFIX}/libexec/${PORTNAME}
 USE_PERL5=	test
 GNU_CONFIGURE=	yes
-SUB_FILES=	pkg-message
 SHEBANG_FILES=	misc/* test/test.pl
 
 OPTIONS_DEFINE=	GPL
@@ -35,18 +36,30 @@ GPL_LIB_DEPENDS=	libgsl.so:math/gsl
 
 .include <bsd.port.options.mk>
 
-CPPFLAGS+=	-I${LOCALBASE}/include
-LDFLAGS+=	-L${LOCALBASE}/lib
-
 .if ${PORT_OPTIONS:MGPL}
 MAKE_ENV+=	USE_GPL=1
-LICENSE=	GPLv3
+LICENSE+=	GPLv3
+LICENSE_COMB=	multi
 .endif
 
 TEST_TARGET=	test
 
 post-patch:
-	@${GREP} -q '@PORTVERSION@' ${WRKSRC}/configure.ac || (echo "@PORTVERSION@ in file/patch-configure.ac is overwritten probably due to using 'make makepatch'"; exit 1)
 	@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
 
+post-install:
+	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/color-chrs.pl \
+		${STAGEDIR}${PREFIX}/bin/color-chrs
+	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/guess-ploidy.py\
+	       ${STAGEDIR}${PREFIX}/bin/guess-ploidy
+	${MV} /${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-roh.py \
+		${STAGEDIR}${PREFIX}/bin/plot-roh
+	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/run-roh.pl \
+		${STAGEDIR}${PREFIX}/bin/run-roh
+	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/vcfutils.pl \
+		${STAGEDIR}${PREFIX}/bin/vcfutils
+	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-vcfstats \
+		${STAGEDIR}${PREFIX}/bin/
+	${RMDIR} ${STAGEDIR}${PREFIX}/bin/samtools_misc/
+
 .include <bsd.port.mk>
diff --git a/biology/bcftools/distinfo b/biology/bcftools/distinfo
index 0f73a5630977..92f009bcffd3 100644
--- a/biology/bcftools/distinfo
+++ b/biology/bcftools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1508307708
-SHA256 (samtools-bcftools-1.6_GH0.tar.gz) = afb2a96d3419fbe77fab5c501dc28bc5e691145353ac5600909a75c0e625f025
-SIZE (samtools-bcftools-1.6_GH0.tar.gz) = 2333330
+TIMESTAMP = 1532903716
+SHA256 (samtools-bcftools-1.9_GH0.tar.gz) = 223b90c9a9b11576174384de70abe8e8394aef1b45c7324e4bf875d0f344e96e
+SIZE (samtools-bcftools-1.9_GH0.tar.gz) = 2394968
diff --git a/biology/bcftools/files/patch-Makefile b/biology/bcftools/files/patch-Makefile
index a79ce1aa4481..6e9f772d2b8b 100644
--- a/biology/bcftools/files/patch-Makefile
+++ b/biology/bcftools/files/patch-Makefile
@@ -1,4 +1,4 @@
---- Makefile.orig	2017-09-28 11:22:48 UTC
+--- Makefile.orig	2018-07-18 08:34:29 UTC
 +++ Makefile
 @@ -22,10 +22,10 @@
  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
@@ -68,10 +68,10 @@
  endif
  
  bcftools: $(OBJS) $(HTSLIB)
-@@ -273,7 +272,7 @@ docs: doc/bcftools.1 doc/bcftools.html
+@@ -278,7 +277,7 @@ docs: doc/bcftools.1 doc/bcftools.html
  # Since there is no make dependency, bcftools.1 can be out-of-date and
  # make docs can be run to update if asciidoc is available
- install: $(PROG) $(PLUGINS)
+ install: $(PROGRAMS) $(PLUGINS)
 -	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
 +	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(misc_bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
  	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
diff --git a/biology/bcftools/files/patch-configure.ac b/biology/bcftools/files/patch-configure.ac
index 40dd18b1099d..ca845d2ad85f 100644
--- a/biology/bcftools/files/patch-configure.ac
+++ b/biology/bcftools/files/patch-configure.ac
@@ -1,10 +1,10 @@
---- configure.ac.orig	2017-09-28 11:22:48 UTC
+--- configure.ac.orig	2018-07-18 08:34:29 UTC
 +++ configure.ac
 @@ -23,7 +23,7 @@
  # DEALINGS IN THE SOFTWARE.
  
  dnl Process this file with autoconf to produce a configure script
--AC_INIT([BCFtools], m4_esyscmd_s([make print-version]),
+-AC_INIT([BCFtools], m4_esyscmd_s([./version.sh 2>/dev/null]),
 +AC_INIT([BCFtools], [@PORTVERSION@],
          [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
  AC_PREREQ([2.63])  dnl This version introduced 4-argument AC_CHECK_HEADER
diff --git a/biology/bcftools/pkg-plist b/biology/bcftools/pkg-plist
index 3c946a32d961..5b68f6191cfb 100644
--- a/biology/bcftools/pkg-plist
+++ b/biology/bcftools/pkg-plist
@@ -1,10 +1,10 @@
 bin/bcftools
-bin/samtools_misc/color-chrs.pl
-bin/samtools_misc/guess-ploidy.py
-bin/samtools_misc/plot-roh.py
-bin/samtools_misc/plot-vcfstats
-bin/samtools_misc/run-roh.pl
-bin/samtools_misc/vcfutils.pl
+bin/color-chrs
+bin/guess-ploidy
+bin/plot-roh
+bin/plot-vcfstats
+bin/run-roh
+bin/vcfutils
 libexec/bcftools/GTisec.so
 libexec/bcftools/GTsubset.so
 libexec/bcftools/ad-bias.so
@@ -12,6 +12,7 @@ libexec/bcftools/af-dist.so
 libexec/bcftools/check-ploidy.so
 libexec/bcftools/check-sparsity.so
 libexec/bcftools/color-chrs.so
+libexec/bcftools/contrast.so
 libexec/bcftools/counts.so
 libexec/bcftools/dosage.so
 libexec/bcftools/fill-AN-AC.so
@@ -27,6 +28,9 @@ libexec/bcftools/mendelian.so
 libexec/bcftools/missing2ref.so
 libexec/bcftools/prune.so
 libexec/bcftools/setGT.so
+libexec/bcftools/smpl-stats.so
+libexec/bcftools/split.so
 libexec/bcftools/tag2tag.so
+libexec/bcftools/trio-stats.so
 libexec/bcftools/trio-switch-rate.so
 man/man1/bcftools.1.gz