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biology/freebayes: Update to 1.3.9
Upstream moved away from git submodules to external deps Several fixes since 1.3.6 Changes: https://github.com/freebayes/freebayes/releases Reported by: portscout
This commit is contained in:
Jason W. Bacon
parent
fc3ebf9794
commit
bac90e855c
3 changed files with 101 additions and 54 deletions
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@ -1,7 +1,6 @@
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PORTNAME= freebayes
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DISTVERSIONPREFIX= v
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DISTVERSION= 1.3.6
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PORTREVISION= 2
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DISTVERSION= 1.3.9
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CATEGORIES= biology
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MAINTAINER= jwb@FreeBSD.org
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@ -10,36 +9,29 @@ WWW= https://github.com/ekg/freebayes
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LICENSE= MIT
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BUILD_DEPENDS= fastahack>=1.0.0:biology/fastahack \
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multichoose>=1.0.3.2:math/multichoose \
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simde>=0.8.2:devel/simde \
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vcflib>=1.0.12:biology/vcflib \
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intervaltree>=0.1.2:devel/intervaltree \
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smithwaterman>=g20160702:biology/smithwaterman \
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wfa2-lib>=2.3.5:biology/wfa2-lib \
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tabixpp>=1.1.2:biology/tabixpp
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LIB_DEPENDS= libhts.so:biology/htslib
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# Submodules use older versions than the ports, so we cannot safely unbundle
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# No shared libs are built by the submodules so there will be no conflicts
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# Yes, there are actually 2 versions of intervaltree required
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USES= compiler:c++14-lang localbase meson perl5 pkgconfig
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USE_GITHUB= yes
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GH_ACCOUNT= ekg
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GH_TUPLE= ekg:intervaltree:b90527f:intervaltree/vcflib/intervaltree \
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ekg:vcflib:d4073c3:vcflib/vcflib-temp \
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ekg:fastahack:bb33265:fastahack/vcflib/fastahack \
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ekg:filevercmp:1a9b779:filevercmp/vcflib/filevercmp \
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ekg:fsom:a6ef318:fsom/vcflib/fsom \
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google:googletest:d225acc:googletest/vcflib/googletest \
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ekg:intervaltree:17ddd57:intervaltree/vcflib/intervaltree \
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edawson:libVCFH:615a06b:libVCFH/vcflib/libVCFH \
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ekg:multichoose:68733cd:multichoose/vcflib/multichoose \
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ekg:smithwaterman:2610e25:smithwaterman/vcflib/smithwaterman \
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ekg:tabixpp:b255df1:tabixpp/vcflib/tabixpp \
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simd-everywhere:simde-no-tests:2931676:simd/vcflib/src/simde \
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ingydotnet:test-simple-bash:124673f:testsimplebash/test/test-simple-bash \
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illusori:bash-tap:c38fbfa:bashtap/test/bash-tap
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USE_PERL5= build
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LDFLAGS+= -lexecinfo
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PLIST_FILES= bin/bamleftalign bin/freebayes
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LDFLAGS+= -lexecinfo
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PLIST_FILES= bin/bamleftalign bin/freebayes
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# GH_TUPLEs cannot seem to share a top-level subdirectory, so we work around
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# by dumping the parent in a temp directory and then moving the contents
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post-extract:
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${CP} -r ${WRKSRC}/vcflib-temp/* ${WRKSRC}/vcflib
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# meson.build is also statically patched, so do this after post-patch.
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# Run make clean patch before updating static patch, to avoid adding
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# up reinplace changes to the static patch.
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pre-configure:
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@${REINPLACE_CMD} -e "s|/usr/local|${PREFIX}|g" ${WRKSRC}/meson.build
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@${REINPLACE_CMD} -e "s|1.3.8|${PORTVERSION}|g" ${WRKSRC}/src/version_git.h
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.include <bsd.port.mk>
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@ -1,29 +1,3 @@
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TIMESTAMP = 1644155282
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SHA256 (ekg-freebayes-v1.3.6_GH0.tar.gz) = d668c0b433cc0f11498ace10e48d72a7f0f40ca23b391b72e975ffafd1c13044
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SIZE (ekg-freebayes-v1.3.6_GH0.tar.gz) = 2898209
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SHA256 (ekg-intervaltree-17ddd57_GH0.tar.gz) = c2274e2382f893241847f75940ad15bac9d1e122da4416b0d2fc61ebba527ee1
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SIZE (ekg-intervaltree-17ddd57_GH0.tar.gz) = 72488
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SHA256 (ekg-vcflib-d4073c3_GH0.tar.gz) = 27ed96714eeaa871b8036bcb308db5256b8266cadd2689fbd1dbf3771611b879
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SIZE (ekg-vcflib-d4073c3_GH0.tar.gz) = 19215364
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SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a
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SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760
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SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070
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SIZE (ekg-filevercmp-1a9b779_GH0.tar.gz) = 3053
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SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b
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SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686
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SHA256 (google-googletest-d225acc_GH0.tar.gz) = 6880e0d51fa80a508ad5674ce483c1c468315faddac10d580b5505e8e7ef6bfa
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SIZE (google-googletest-d225acc_GH0.tar.gz) = 1279815
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SHA256 (edawson-libVCFH-615a06b_GH0.tar.gz) = 2774c26c55e1d155fe803b492a745a1d2a3659f4fdbe248d3187ce03edf87223
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SIZE (edawson-libVCFH-615a06b_GH0.tar.gz) = 2295
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SHA256 (ekg-multichoose-68733cd_GH0.tar.gz) = 909baf2e462e43e71ba0d015fbe759c0ab95331c36d6c4ec65e4a92a7b9d3297
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SIZE (ekg-multichoose-68733cd_GH0.tar.gz) = 6558
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SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce
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SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160
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SHA256 (ekg-tabixpp-b255df1_GH0.tar.gz) = 96d9aa41f55f74498e267b582e93e986605913fbd830dca6bf4cac5d9f927bb9
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SIZE (ekg-tabixpp-b255df1_GH0.tar.gz) = 3739
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SHA256 (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 3877e64f51a7368f768b40167e4cdff36a93d3047f722416581834f1eaf40f63
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SIZE (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 203996
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SHA256 (ingydotnet-test-simple-bash-124673f_GH0.tar.gz) = 19b5c27402d955909fcbf601ed02bcd7d9f2aa841e2158ecd93b9ff8f7ec1d98
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SIZE (ingydotnet-test-simple-bash-124673f_GH0.tar.gz) = 6609
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SHA256 (illusori-bash-tap-c38fbfa_GH0.tar.gz) = 5e658965f7c8730d7f29642ebb40b0e0beb701f992e391a1273af3b132ff66b8
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SIZE (illusori-bash-tap-c38fbfa_GH0.tar.gz) = 5826
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TIMESTAMP = 1739833701
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SHA256 (ekg-freebayes-v1.3.9_GH0.tar.gz) = 41ed3074c7648375286168a6708e02dac6788eaca4ca6039ff5a7ed91f257b53
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SIZE (ekg-freebayes-v1.3.9_GH0.tar.gz) = 2896143
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81
biology/freebayes/files/patch-meson.build
Normal file
81
biology/freebayes/files/patch-meson.build
Normal file
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@ -0,0 +1,81 @@
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--- meson.build.orig 2025-02-16 14:02:36 UTC
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+++ meson.build
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@@ -15,7 +15,7 @@ project('freebayes', ['cpp', 'c'],
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project('freebayes', ['cpp', 'c'],
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version : '1.3.9',
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- default_options : ['warning_level=1', 'cpp_std=c++17', 'optimization=3'])
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+ default_options : ['warning_level=1', 'cpp_std=c++14', 'optimization=3'])
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static_build = get_option('static')
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# used by Debian: add_global_arguments('-D_GLIBCXX_ASSERTIONS=1', language : 'cpp')
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@@ -25,10 +25,12 @@ thread_dep = dependency('threads', static: static_buil
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# fastahack_dep = cc.find_library('libfastahack')
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lzma_dep = dependency('liblzma', static: static_build)
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thread_dep = dependency('threads', static: static_build)
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-wfa2lib_dep = cc.find_library('libwfa2') # need to link for vcflib code
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+wfa2_inc = include_directories('/usr/local/include/wfa2lib')
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+wfa2lib_dep = declare_dependency(include_directories: wfa2_inc)
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zlib_dep = dependency('zlib', static: static_build)
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htslib_dep = dependency('htslib', static: static_build, required: false)
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-vcflib_dep = cc.find_library('libvcflib', required: false)
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+vcflib_inc = include_directories('/usr/local/include/vcflib')
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+vcflib_dep = declare_dependency(link_args: '-lvcflib', include_directories: vcflib_inc)
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seqlib_dep = dependency('libseqlib', static: static_build, required: false)
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tabixpp_dep = cc.find_library('tabixpp', required: false, static: static_build)
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@@ -43,14 +45,12 @@ if get_option('prefer_system_deps') # defaults to true
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if get_option('prefer_system_deps') # defaults to true, otherwise use git modules and local sources
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- fastahack_dep = cc.find_library('libfastahack', required: true) # also link in for vcflib
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- smithwaterman_dep = cc.find_library('libsmithwaterman')
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- if fs.is_dir('/usr/include/fastahack')
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- message('Using /usr/include/fastahack dir')
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- fastahack_inc = include_directories('/usr/include/fastahack')
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- else
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- fastahack_inc = files()
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- endif
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+ fastahack_inc = include_directories('/usr/local/include/fastahack')
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+ fastahack_dep = declare_dependency(include_directories: fastahack_inc)
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+ sw_inc = include_directories('/usr/local/include/smithwaterman')
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+ smithwaterman_dep = declare_dependency(include_directories: sw_inc)
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+ multichoose_inc = include_directories('/usr/local/include/multichoose')
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+ multichoose_dep = declare_dependency(include_directories: multichoose_inc)
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else
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# uses the minimal local git submodules or checkout trees in ./contrib/
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@@ -153,14 +153,14 @@ freebayes_lib = static_library(
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include_directories : [incdir, vcflib_inc, fastahack_inc],
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cpp_args : extra_cpp_args,
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dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep,
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- vcflib_dep, wfa2lib_dep, seqlib_dep],
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+ vcflib_dep, wfa2lib_dep, seqlib_dep, multichoose_dep],
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install : false,
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)
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if static_build
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- link_arguments = '-static'
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+ link_arguments = '-static -L/usr/local/lib'
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else
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- link_arguments = []
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+ link_arguments = '-L/usr/local/lib'
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endif
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executable('freebayes',
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@@ -177,6 +177,7 @@ executable('freebayes',
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seqlib_dep,
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fastahack_dep, # for vcflib
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smithwaterman_dep, # for vcflib
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+ multichoose_dep,
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wfa2lib_dep],
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link_with : freebayes_lib,
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install: true
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@@ -195,6 +196,7 @@ executable('bamleftalign',
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seqlib_dep,
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fastahack_dep, # for vcflib
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smithwaterman_dep, # for vcflib
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+ multichoose_dep,
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wfa2lib_dep],
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link_with : freebayes_lib,
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install: true
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