diff options
Diffstat (limited to 'biology/htslib')
| -rw-r--r-- | biology/htslib/Makefile | 10 | ||||
| -rw-r--r-- | biology/htslib/distinfo | 6 | ||||
| -rw-r--r-- | biology/htslib/files/patch-Makefile | 37 | ||||
| -rw-r--r-- | biology/htslib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c | 11 | ||||
| -rw-r--r-- | biology/htslib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c | 11 | ||||
| -rw-r--r-- | biology/htslib/pkg-descr | 2 | ||||
| -rw-r--r-- | biology/htslib/pkg-plist | 14 |
7 files changed, 48 insertions, 43 deletions
diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile index ec7ab0ab4d8d..5a844cef433c 100644 --- a/biology/htslib/Makefile +++ b/biology/htslib/Makefile @@ -1,13 +1,13 @@ -# Created by: Reed A. Cartwright <cartwright@asu.edu> - PORTNAME= htslib -DISTVERSION= 1.13 +DISTVERSION= 1.17 +PORTREVISION= 1 CATEGORIES= biology devel # Github generated distfiles are incomplete, so use custom tarball MASTER_SITES= https://github.com/samtools/htslib/releases/download/${DISTVERSION}/ MAINTAINER= jwb@FreeBSD.org COMMENT= C library for high-throughput sequencing data formats +WWW= https://www.htslib.org/ LICENSE= BSD3CLAUSE MIT LICENSE_COMB= multi @@ -21,6 +21,10 @@ USE_PERL5= test USE_LDCONFIG= yes GNU_CONFIGURE= yes +GNU_CONFIGURE_MANPREFIX=${PREFIX}/share +MAKE_ARGS_armv6= HTS_HAVE_NEON= +MAKE_ARGS_armv7= HTS_HAVE_NEON= +MAKE_ARGS= $(MAKE_ARGS_$(ARCH)) PATHFIX_MAKEFILEIN= Makefile SHEBANG_FILES= test/*.pl diff --git a/biology/htslib/distinfo b/biology/htslib/distinfo index dc4bf1b4ea09..24c398cacc3c 100644 --- a/biology/htslib/distinfo +++ b/biology/htslib/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1626039683 -SHA256 (htslib-1.13.tar.bz2) = f2407df9f97f0bb6b07656579e41a1ca5100464067b6b21bf962a2ea4b0efd65 -SIZE (htslib-1.13.tar.bz2) = 4226834 +TIMESTAMP = 1677245487 +SHA256 (htslib-1.17.tar.bz2) = 763779288c40f07646ec7ad98b96c378c739171d162ad98398868783b721839f +SIZE (htslib-1.17.tar.bz2) = 4619884 diff --git a/biology/htslib/files/patch-Makefile b/biology/htslib/files/patch-Makefile index 7f91465d2ccd..eb6fb7f85901 100644 --- a/biology/htslib/files/patch-Makefile +++ b/biology/htslib/files/patch-Makefile @@ -1,33 +1,14 @@ ---- Makefile.orig 2021-03-20 15:53:14 UTC +--- Makefile.orig 2023-02-24 13:35:28 UTC +++ Makefile -@@ -53,13 +53,14 @@ man5dir = $(mandir)/man5 - man7dir = $(mandir)/man7 - pkgconfigdir= $(prefix)/libdata/pkgconfig - --MKDIR_P = mkdir -p --INSTALL = install -p --INSTALL_DATA = $(INSTALL) -m 644 --INSTALL_DIR = $(MKDIR_P) -m 755 --INSTALL_LIB = $(INSTALL_DATA) --INSTALL_MAN = $(INSTALL_DATA) +@@ -60,9 +60,9 @@ INSTALL = install -p + INSTALL_DATA = $(INSTALL) -m 644 + INSTALL_DIR = $(MKDIR_P) -m 755 + LIB_PERM = 644 +-INSTALL_LIB = $(INSTALL) -m $(LIB_PERM) ++INSTALL_LIB = $(BSD_INSTALL_LIB) + INSTALL_MAN = $(INSTALL_DATA) -INSTALL_PROGRAM = $(INSTALL) -+# Use ports BSD_INSTALL_PROGRAM to strip if WITH_DEBUG is not set -+MKDIR_P = mkdir -p -+INSTALL = install -p -+INSTALL_DATA = ${BSD_INSTALL_DATA} -+INSTALL_DIR = $(MKDIR_P) -+INSTALL_LIB = ${BSD_INSTALL_LIB} -+INSTALL_MAN = ${BSD_INSTALL_MAN} -+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} ++INSTALL_PROGRAM = $(BSD_INSTALL_PROGRAM) # Set by config.mk if plugins are enabled plugindir = -@@ -102,7 +103,7 @@ BUILT_THRASH_PROGRAMS = \ - test/thrash_threads6 \ - test/thrash_threads7 - --all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) \ -+all: lib-static lib-shared $(BUILT_PROGRAMS) plugins \ - htslib_static.mk htslib-uninstalled.pc - - ALL_CPPFLAGS = -I. $(CPPFLAGS) diff --git a/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c b/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c new file mode 100644 index 000000000000..577a3d651321 --- /dev/null +++ b/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static32x16pr__neon.c @@ -0,0 +1,11 @@ +--- htscodecs/htscodecs/rANS_static32x16pr_neon.c.orig 2023-04-17 21:11:08 UTC ++++ htscodecs/htscodecs/rANS_static32x16pr_neon.c +@@ -32,7 +32,7 @@ + */ + + #include "config.h" +-#ifdef __ARM_NEON ++#if defined(__ARM_NEON) && defined(__aarch64__) + #include <arm_neon.h> + + #include <limits.h> diff --git a/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c b/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c new file mode 100644 index 000000000000..8f3e883eec42 --- /dev/null +++ b/biology/htslib/files/patch-htscodecs_htscodecs_rANS__static4x16pr.c @@ -0,0 +1,11 @@ +--- htscodecs/htscodecs/rANS_static4x16pr.c.orig 2023-04-17 21:13:50 UTC ++++ htscodecs/htscodecs/rANS_static4x16pr.c +@@ -1006,7 +1006,7 @@ unsigned char *(*rans_dec_func(int do_simd, int order) + } + } + +-#elif defined(__ARM_NEON) ++#elif defined(__ARM_NEON) && defined(__aarch64__) + + #if defined(__linux__) || defined(__FreeBSD__) + #include <sys/auxv.h> diff --git a/biology/htslib/pkg-descr b/biology/htslib/pkg-descr index f5684283ff81..050ad06ba93e 100644 --- a/biology/htslib/pkg-descr +++ b/biology/htslib/pkg-descr @@ -1,5 +1,3 @@ HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing data. It is the core library used by samtools and bcftools. - -WWW: https://www.htslib.org/ diff --git a/biology/htslib/pkg-plist b/biology/htslib/pkg-plist index e2ebe3a2e8d6..8c97aa84399c 100644 --- a/biology/htslib/pkg-plist +++ b/biology/htslib/pkg-plist @@ -34,10 +34,10 @@ lib/libhts.so lib/libhts.so.%%PORTVERSION%% lib/libhts.so.3 libdata/pkgconfig/htslib.pc -man/man1/bgzip.1.gz -man/man1/htsfile.1.gz -man/man1/tabix.1.gz -man/man5/faidx.5.gz -man/man5/sam.5.gz -man/man5/vcf.5.gz -man/man7/htslib-s3-plugin.7.gz +share/man/man1/bgzip.1.gz +share/man/man1/htsfile.1.gz +share/man/man1/tabix.1.gz +share/man/man5/faidx.5.gz +share/man/man5/sam.5.gz +share/man/man5/vcf.5.gz +share/man/man7/htslib-s3-plugin.7.gz |