mirror of
https://git.FreeBSD.org/ports.git
synced 2025-01-04 06:15:24 +00:00
biology/vcflib: Update to 1.0.12
A few fixes and enhancements Changes: https://github.com/vcflib/vcflib/releases Reported by: portscout
This commit is contained in:
Jason W. Bacon
parent
db1d0b8c1c
commit
3f6b18bb38
@ -1,6 +1,6 @@
|
||||
PORTNAME= vcflib
|
||||
DISTVERSIONPREFIX= v
|
||||
DISTVERSION= 1.0.10
|
||||
DISTVERSION= 1.0.12
|
||||
CATEGORIES= biology
|
||||
|
||||
MAINTAINER= jwb@FreeBSD.org
|
||||
@ -12,7 +12,8 @@ LICENSE= MIT
|
||||
NOT_FOR_ARCHS= armv6 armv7
|
||||
NOT_FOR_ARCHS_REASON= requires OpenMP which is not supported
|
||||
|
||||
BUILD_DEPENDS= pybind11>0:devel/pybind11
|
||||
BUILD_DEPENDS= pybind11>0:devel/pybind11 \
|
||||
${PYTHON_PKGNAMEPREFIX}pypandoc>=1.4:textproc/py-pypandoc@${PY_FLAVOR}
|
||||
LIB_DEPENDS= libhts.so:biology/htslib \
|
||||
libcurl.so:ftp/curl \
|
||||
libwfa2.so:biology/wfa2-lib
|
||||
@ -29,7 +30,7 @@ GH_TUPLE= ekg:fastahack:bb33265:fastahack/contrib/fastahack \
|
||||
ekg:multichoose:e1f94ae:multichoose/contrib/multichoose \
|
||||
ekg:smithwaterman:2610e25:smithwaterman/contrib/smithwaterman \
|
||||
simd-everywhere:simde-no-tests:9af03cd:simd/src/simde \
|
||||
vcflib:tabixpp:v1.1.2:tabixpp/contrib/tabixpp
|
||||
vcflib:tabixpp:ae5cdf8:tabixpp/contrib/tabixpp
|
||||
SHEBANG_FILES= scripts/*
|
||||
|
||||
# FIXME: Add Zig option + lang/zig dep
|
||||
@ -39,10 +40,9 @@ OPTIONS_SUB= yes
|
||||
|
||||
ZIG_DESC= Include Zig language support
|
||||
|
||||
# FIXME: https://github.com/vcflib/vcflib/issues/399
|
||||
ZIG_BUILD_DEPENDS= zig010>0:lang/zig010
|
||||
ZIG_BUILD_DEPENDS= zig>0:lang/zig
|
||||
|
||||
CMAKE_ARGS+= -DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so
|
||||
CMAKE_ARGS+= -DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so.0
|
||||
ZIG_CMAKE_OFF= -DZIG=OFF
|
||||
|
||||
# Clang and GCC disable sse2 by default on i386, but it's required for vcflib
|
||||
|
||||
@ -1,6 +1,6 @@
|
||||
TIMESTAMP = 1713703391
|
||||
SHA256 (ekg-vcflib-v1.0.10_GH0.tar.gz) = 6f7f366555e5b191a509bda6d7a2078825827458ba7e9922094c4c1ebb48e693
|
||||
SIZE (ekg-vcflib-v1.0.10_GH0.tar.gz) = 23539349
|
||||
TIMESTAMP = 1732541764
|
||||
SHA256 (ekg-vcflib-v1.0.12_GH0.tar.gz) = 7ab5b6a87a39105107029f5e0da52ece612c71095ab2aec69a00320f44bc5300
|
||||
SIZE (ekg-vcflib-v1.0.12_GH0.tar.gz) = 23543176
|
||||
SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a
|
||||
SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760
|
||||
SHA256 (ekg-filevercmp-df20dcc_GH0.tar.gz) = d34bec614be638e05eb6fa419c936b9e7de58d50b1a096a5ca02aadb7db6b059
|
||||
@ -17,5 +17,5 @@ SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905
|
||||
SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160
|
||||
SHA256 (simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz) = 99dcb7d6a2e1dc3f51401ff16eaa5dde93c793e13b514ea9cae4d9819144b8fe
|
||||
SIZE (simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz) = 572867
|
||||
SHA256 (vcflib-tabixpp-v1.1.2_GH0.tar.gz) = c850299c3c495221818a85c9205c60185c8ed9468d5ec2ed034470bb852229dc
|
||||
SIZE (vcflib-tabixpp-v1.1.2_GH0.tar.gz) = 6962
|
||||
SHA256 (vcflib-tabixpp-ae5cdf8_GH0.tar.gz) = edb15012b57c6bfc900c1b8275fc3d55f2e7c21e83601f8cfedcbdf3107fbb04
|
||||
SIZE (vcflib-tabixpp-ae5cdf8_GH0.tar.gz) = 6965
|
||||
|
||||
@ -1,15 +1,6 @@
|
||||
--- CMakeLists.txt.orig 2023-02-07 17:22:46 UTC
|
||||
--- CMakeLists.txt.orig 2024-11-21 07:59:50 UTC
|
||||
+++ CMakeLists.txt
|
||||
@@ -9,7 +9,7 @@ project(vcflib)
|
||||
cmake_minimum_required(VERSION 3.16)
|
||||
project(vcflib)
|
||||
|
||||
-set(CMAKE_CXX_STANDARD 17)
|
||||
+set(CMAKE_CXX_STANDARD 14)
|
||||
|
||||
include(ExternalProject)
|
||||
include(FeatureSummary)
|
||||
@@ -69,7 +69,7 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release)
|
||||
@@ -70,7 +70,7 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release)
|
||||
endif()
|
||||
|
||||
if (${CMAKE_BUILD_TYPE} MATCHES Release)
|
||||
@ -18,9 +9,14 @@
|
||||
# set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast
|
||||
endif()
|
||||
|
||||
@@ -570,4 +570,4 @@ install(FILES ${INCLUDES} DESTINATION include)
|
||||
@@ -595,8 +595,8 @@ install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INS
|
||||
# ---- Install
|
||||
|
||||
install(FILES ${INCLUDES} DESTINATION include)
|
||||
install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
-install(TARGETS ${WFALIB} ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
+# install(TARGETS ${WFALIB} ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
|
||||
install(FILES ${INCLUDES} DESTINATION include/vcflib)
|
||||
|
||||
-install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/man/man1)
|
||||
+install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/man/man1)
|
||||
|
||||
@ -26,7 +26,6 @@ bin/vcf2tsv
|
||||
bin/vcf_strip_extra_headers
|
||||
bin/vcfaddinfo
|
||||
bin/vcfafpath
|
||||
bin/vcfallelicprimitives
|
||||
bin/vcfaltcount
|
||||
bin/vcfannotate
|
||||
bin/vcfannotategenotypes
|
||||
@ -35,7 +34,6 @@ bin/vcfbreakmulti
|
||||
bin/vcfcat
|
||||
bin/vcfcheck
|
||||
bin/vcfclassify
|
||||
bin/vcfcleancomplex
|
||||
bin/vcfclearid
|
||||
bin/vcfclearinfo
|
||||
bin/vcfcombine
|
||||
@ -85,7 +83,6 @@ bin/vcfnulldotslashdot
|
||||
bin/vcfnullgenofields
|
||||
bin/vcfnumalt
|
||||
bin/vcfoverlay
|
||||
bin/vcfparsealts
|
||||
bin/vcfplotaltdiscrepancy.r
|
||||
bin/vcfplotaltdiscrepancy.sh
|
||||
bin/vcfplotsitediscrepancy.r
|
||||
@ -105,59 +102,57 @@ bin/vcfremap
|
||||
bin/vcfremoveaberrantgenotypes
|
||||
bin/vcfremovenonATGC
|
||||
bin/vcfremovesamples
|
||||
bin/vcfroc
|
||||
bin/vcfsample2info
|
||||
bin/vcfsamplediff
|
||||
bin/vcfsamplenames
|
||||
bin/vcfsitesummarize
|
||||
bin/vcfsnps
|
||||
bin/vcfsort
|
||||
bin/vcfstats
|
||||
bin/vcfstreamsort
|
||||
bin/vcfuniq
|
||||
bin/vcfuniqalleles
|
||||
bin/vcfvarstats
|
||||
bin/vcfwave
|
||||
bin/wcFst
|
||||
include/BandedSmithWaterman.h
|
||||
include/BedReader.h
|
||||
include/Fasta.h
|
||||
include/IndelAllele.h
|
||||
include/IntervalTree.h
|
||||
include/LargeFileSupport.h
|
||||
include/LeftAlign.h
|
||||
include/LeftAlign.hpp
|
||||
include/Mosaik.h
|
||||
include/Region.h
|
||||
include/Repeats.h
|
||||
include/SmithWatermanGotoh.h
|
||||
include/Variant.h
|
||||
include/allele.hpp
|
||||
include/catch.hpp
|
||||
include/cdflib.hpp
|
||||
include/cigar.hpp
|
||||
include/convert.h
|
||||
include/disorder.h
|
||||
include/filevercmp.h
|
||||
include/gpatInfo.hpp
|
||||
include/join.h
|
||||
include/makeUnique.h
|
||||
include/mt19937ar.h
|
||||
include/multichoose.h
|
||||
include/multipermute.h
|
||||
include/murmur3.hpp
|
||||
include/pdflib.hpp
|
||||
include/rkmh.hpp
|
||||
include/rnglib.hpp
|
||||
include/split.h
|
||||
include/ssw.hpp
|
||||
include/ssw_cpp.hpp
|
||||
include/var.hpp
|
||||
include/vcf-c-api.h
|
||||
include/vcf-wfa.h
|
||||
include/vcflib/BandedSmithWaterman.h
|
||||
include/vcflib/BedReader.h
|
||||
include/vcflib/Fasta.h
|
||||
include/vcflib/IndelAllele.h
|
||||
include/vcflib/IntervalTree.h
|
||||
include/vcflib/LargeFileSupport.h
|
||||
include/vcflib/LeftAlign.h
|
||||
include/vcflib/LeftAlign.hpp
|
||||
include/vcflib/Mosaik.h
|
||||
include/vcflib/Region.h
|
||||
include/vcflib/Repeats.h
|
||||
include/vcflib/SmithWatermanGotoh.h
|
||||
include/vcflib/Variant.h
|
||||
include/vcflib/allele.hpp
|
||||
include/vcflib/canonicalize.h
|
||||
include/vcflib/catch.hpp
|
||||
include/vcflib/cdflib.hpp
|
||||
include/vcflib/cigar.hpp
|
||||
include/vcflib/convert.h
|
||||
include/vcflib/disorder.h
|
||||
include/vcflib/filevercmp.h
|
||||
include/vcflib/gpatInfo.hpp
|
||||
include/vcflib/join.h
|
||||
include/vcflib/legacy.h
|
||||
include/vcflib/makeUnique.h
|
||||
include/vcflib/mt19937ar.h
|
||||
include/vcflib/multichoose.h
|
||||
include/vcflib/murmur3.hpp
|
||||
include/vcflib/pdflib.hpp
|
||||
include/vcflib/rkmh.hpp
|
||||
include/vcflib/rnglib.hpp
|
||||
include/vcflib/split.h
|
||||
include/vcflib/ssw.hpp
|
||||
include/vcflib/ssw_cpp.hpp
|
||||
include/vcflib/var.hpp
|
||||
include/vcflib/vcf-c-api.h
|
||||
include/vcflib/vcf-wfa.h
|
||||
lib/libvcflib.a
|
||||
%%ZIG%%lib/libzig.a
|
||||
lib/pyvcflib%%PYTHON_EXT_SUFFIX%%.so
|
||||
%%ZIG%%lib/libzig.a
|
||||
share/man/man1/abba-baba.1.gz
|
||||
share/man/man1/bFst.1.gz
|
||||
share/man/man1/dumpContigsFromHeader.1.gz
|
||||
|
||||
Loading…
Reference in New Issue
Block a user