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biology/bcftools: Update to 1.21

Browse source 
Numerous bug fixes and enhancements since 1.17
Changes:        https://github.com/samtools/bcftools/releases

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2024-10-09 17:12:12 -05:00
parent c9894f6009
commit 6a3ed7c424
4 changed files with 19 additions and 22 deletions
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5
biology/bcftools/Makefile
View file

@ -1,6 +1,5 @@
PORTNAME= bcftools
PORTVERSION= 1.17
PORTREVISION= 1
PORTVERSION= 1.21
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
@ -10,6 +9,7 @@ WWW= https://www.htslib.org/
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= htslib>=1.21:biology/htslib
LIB_DEPENDS= libhts.so:biology/htslib
TEST_DEPENDS= bash:shells/bash
RUN_DEPENDS= bash:shells/bash
@ -17,7 +17,6 @@ RUN_DEPENDS= bash:shells/bash
USES= autoreconf gmake localbase perl5 python:env shebangfix
USE_GITHUB= yes
USE_PERL5= test
GH_ACCOUNT= samtools
GNU_CONFIGURE= yes

6
biology/bcftools/distinfo
View file

@ -1,3 +1,3 @@
TIMESTAMP = 1677246068
SHA256 (samtools-bcftools-1.17_GH0.tar.gz) = e6fdb4c94b531671ea8a0b00cb9245aa2602f6c4480621e45dac76338f590b9e
SIZE (samtools-bcftools-1.17_GH0.tar.gz) = 3481344
TIMESTAMP = 1727437561
SHA256 (samtools-bcftools-1.21_GH0.tar.gz) = 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d
SIZE (samtools-bcftools-1.21_GH0.tar.gz) = 3665160

29
biology/bcftools/files/patch-Makefile
View file

@ -1,6 +1,6 @@
--- Makefile.orig 2021-03-17 09:16:18 UTC
--- Makefile.orig 2024-09-27 11:44:03 UTC
+++ Makefile
@@ -58,13 +58,14 @@ pluginpath = $(plugindir)
@@ -59,13 +59,13 @@ misc_bindir = $(bindir)
# Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
misc_bindir = $(bindir)
@ -11,23 +11,22 @@
-INSTALL_MAN = $(INSTALL_DATA)
-INSTALL_PROGRAM = $(INSTALL)
-INSTALL_SCRIPT = $(INSTALL_PROGRAM)
+# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set
+MKDIR_P = mkdir -p
+INSTALL = install -p
+INSTALL_DATA = ${BSD_INSTALL_DATA}
+INSTALL_DIR = $(MKDIR_P)
+INSTALL_MAN = ${BSD_INSTALL_MAN}
+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
+INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT}
+MKDIR_P = mkdir -p
+INSTALL = install -p
+INSTALL_DATA = ${BSD_INSTALL_DATA}
+INSTALL_DIR = $(MKDIR_P)
+INSTALL_MAN = ${BSD_INSTALL_MAN}
+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
+INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT}
PROGRAMS = bcftools
MISC_SCRIPTS = \
@@ -142,7 +143,7 @@ print-version:
ifdef USE_GPL
@@ -144,7 +144,7 @@ ifdef USE_GPL
main.o : EXTRA_CPPFLAGS += -DUSE_GPL
OBJS += polysomy.o peakfit.o
- GSL_LIBS ?= -lgsl -lcblas
+ GSL_LIBS ?= -lgslcblas
ifndef GSL_LIBS
- GSL_LIBS += -lgsl -lcblas
+ GSL_LIBS += -lgslcblas
endif
endif
print-%:

1
biology/bcftools/pkg-plist
View file

@ -29,7 +29,6 @@ libexec/bcftools/gvcfz.so
libexec/bcftools/impute-info.so
libexec/bcftools/indel-stats.so
libexec/bcftools/isecGT.so
libexec/bcftools/mendelian.so
libexec/bcftools/mendelian2.so
libexec/bcftools/missing2ref.so
libexec/bcftools/parental-origin.so