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99043adf46
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Remove vcflib-source, intervaltree-source. Move vcflib ... [inputs]: ... to here. [arguments]: Adjust 'patch-source and 'unpack-submodule-sources for changes in vendored code. * gnu/packages/patches/freebayes-devendor-deps.patch: Update patch.
152 lines
4 KiB
Diff
152 lines
4 KiB
Diff
This patch is original to Guix, ongoing work to upstream bits as possible.
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From 9acc56db5e7469f5976be38b52ba4993de98ee38 Mon Sep 17 00:00:00 2001
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From: Efraim Flashner <efraim@flashner.co.il>
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Date: Sun, 17 Jan 2021 13:27:17 +0200
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Subject: [PATCH] devendor-dependants
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---
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meson.build | 84 +++++++++++++++++++++++++++++++++++++++++------------
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1 file changed, 66 insertions(+), 18 deletions(-)
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diff --git a/meson.build b/meson.build
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index f6bf242..bded4af 100644
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--- a/meson.build
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+++ b/meson.build
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@@ -9,8 +9,13 @@ project('freebayes', ['cpp', 'c'],
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zlib_dep = dependency('zlib')
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lzma_dep = dependency('liblzma')
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+simde_dep = dependency('simde')
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bzip2_dep = dependency('bz2lib', required: false)
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htslib_dep = dependency('htslib', required : false)
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+tabixpp_dep = dependency('tabixpp', required : false)
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+fastahack_dep = dependency('fastahack', required : false)
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+smithwaterman_dep = dependency('smithwaterman', required : false)
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+vcflib_dep = dependency('libvcflib', required: false)
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thread_dep = dependency('threads')
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if htslib_dep.found()
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@@ -59,6 +64,56 @@ else
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]
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endif
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+if tabixpp_dep.found()
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+ tabixpp_includes = ''
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+ tabixpp_src = []
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+else
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+ tabixpp_includes = [
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+ 'vcflib/tabixpp',
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+ ]
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+ tabixpp_src = [
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+ 'vcflib/tabixpp/tabix.cpp',
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+ ]
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+endif
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+
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+if vcflib_dep.found()
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+ vcflib_includes = ''
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+ vcflib_src = []
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+else
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+ vcflib_includes = [
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+ 'vcflib/src',
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+ 'vcflib/multichoose',
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+ 'vcflib/filevercmp',
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+ ]
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+ vcflib_src = [
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+ 'vcflib/src/Variant.cpp',
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+ ]
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+endif
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+
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+if fastahack_dep.found()
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+ fastahack_src = []
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+else
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+ fastahack_src = [
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+ 'vcflib/fastahack/Fasta.cpp',
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+ 'vcflib/src/split.cpp',
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+ ]
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+endif
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+
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+if smithwaterman_dep.found()
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+ smithwaterman_includes = ''
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+ smithwaterman_src = []
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+else
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+ smithwaterman_includes = [
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+ 'vcflib/smithwaterman',
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+ ]
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+ smithwaterman_src = [
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+ 'vcflib/smithwaterman/SmithWatermanGotoh.cpp',
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+ 'vcflib/smithwaterman/disorder.cpp',
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+ 'vcflib/smithwaterman/Repeats.cpp',
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+ 'vcflib/smithwaterman/LeftAlign.cpp',
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+ 'vcflib/smithwaterman/IndelAllele.cpp',
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+ ]
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+endif
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#
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@@ -105,23 +160,18 @@ seqlib_src = [
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]
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vcflib_src = [
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- 'vcflib/tabixpp/tabix.cpp',
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- 'vcflib/src/Variant.cpp',
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- 'vcflib/smithwaterman/SmithWatermanGotoh.cpp',
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- 'vcflib/smithwaterman/disorder.cpp',
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- 'vcflib/smithwaterman/Repeats.cpp',
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- 'vcflib/smithwaterman/LeftAlign.cpp',
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- 'vcflib/smithwaterman/IndelAllele.cpp',
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+ vcflib_src,
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+ tabixpp_src,
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+ smithwaterman_src,
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]
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bamleftalign_src = [
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'src/bamleftalign.cpp',
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'src/IndelAllele.cpp',
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'contrib/SeqLib/src/BamWriter.cpp',
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- 'vcflib/fastahack/Fasta.cpp',
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- 'vcflib/smithwaterman/LeftAlign.cpp',
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- 'vcflib/smithwaterman/IndelAllele.cpp',
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- 'vcflib/src/split.cpp',
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+ fastahack_src,
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+ smithwaterman_src,
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+ vcflib_src,
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'src/LeftAlign.cpp',
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]
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@@ -134,11 +184,9 @@ incdir = include_directories(
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'ttmath',
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'contrib',
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'contrib/SeqLib',
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- 'vcflib/src',
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- 'vcflib/tabixpp',
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- 'vcflib/smithwaterman',
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- 'vcflib/multichoose',
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- 'vcflib/filevercmp')
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+ tabixpp_includes,
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+ smithwaterman_includes,
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+ vcflib_includes)
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c_args = ['-fpermissive','-w']
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cpp_args = ['-fpermissive','-w','-Wc++14-compat']
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@@ -152,7 +200,7 @@ executable('freebayes',
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include_directories : incdir,
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cpp_args : cpp_args,
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c_args : c_args,
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- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep],
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+ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, smithwaterman_dep, vcflib_dep, thread_dep],
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install: true
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)
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@@ -165,7 +213,7 @@ executable('bamleftalign',
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include_directories : incdir,
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cpp_args : cpp_args,
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c_args : c_args,
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- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep],
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+ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, fastahack_dep, smithwaterman_dep, vcflib_dep, thread_dep],
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install: true
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)
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--
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2.30.0
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