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Index: biology/bcftools/Makefile
===================================================================
--- biology/bcftools/Makefile
+++ 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 @@
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 @@
.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>
Index: biology/bcftools/distinfo
===================================================================
--- biology/bcftools/distinfo
+++ 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
Index: biology/bcftools/files/patch-Makefile
===================================================================
--- biology/bcftools/files/patch-Makefile
+++ 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)
Index: biology/bcftools/files/patch-configure.ac
===================================================================
--- biology/bcftools/files/patch-configure.ac
+++ 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
Index: biology/bcftools/pkg-plist
===================================================================
--- biology/bcftools/pkg-plist
+++ 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/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/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

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