gnu: freebayes: Don't include vcflib sources.
* 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.
This commit is contained in:
Efraim Flashner
parent
1bbfe1789d
commit
99043adf46
@ -15138,6 +15138,7 @@ manipulations on VCF files.")
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("htslib" ,htslib)
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("smithwaterman" ,smithwaterman)
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("tabixpp" ,tabixpp)
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("vcflib" ,vcflib)
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("zlib" ,zlib)))
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(native-inputs
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`(("bash-tap" ,bash-tap)
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@ -15148,11 +15149,6 @@ manipulations on VCF files.")
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("pkg-config" ,pkg-config)
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("samtools" ,samtools)
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("simde" ,simde)
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;; We need some binaries from vcflib, but we also need to link against a
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;; subset of the library. Vendor the parts we need until we have a shared library.
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("vcflib" ,vcflib)
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("vcflib-src" ,(package-source vcflib))
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("intervaltree-src" ,(package-source intervaltree))
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;; This submodule is needed to run the tests.
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("test-simple-bash-src"
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,(origin
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@ -15179,25 +15175,17 @@ manipulations on VCF files.")
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(substitute* "meson.build"
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;; Some inputs aren't actually needed.
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((".*bamtools/src.*") "")
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((".*multichoose.*") "")
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(("'vcflib/filevercmp'") ""))
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((".*multichoose.*") ""))
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(substitute* '("src/BedReader.cpp"
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"src/BedReader.h")
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(("../intervaltree/IntervalTree.h") "IntervalTree.h"))
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#t)))
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(add-after 'unpack 'unpack-submodule-sources
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((unpack (lambda (source target)
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(unless (directory-exists? target)
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(mkdir-p target))
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(with-directory-excursion target
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(if (file-is-directory? (assoc-ref inputs source))
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(copy-recursively (assoc-ref inputs source) ".")
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(invoke "tar" "xvf"
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(assoc-ref inputs source)
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"--strip-components=1"))))))
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(and
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(unpack "vcflib-src" "vcflib")
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(unpack "intervaltree-src" "vcflib/intervaltree")
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(unpack "test-simple-bash-src" "test/test-simple-bash"))
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#t)))
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(mkdir-p "test/test-simple-bash")
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(copy-recursively (assoc-ref inputs "test-simple-bash-src")
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"test/test-simple-bash")
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#t))
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;; The slow tests take longer than the specified timeout.
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,@(if (any (cute string=? <> (%current-system))
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'("armhf-linux" "aarch64-linux"))
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@ -1,19 +1,19 @@
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This patch is original to Guix, ongoing work to upstream bits as possible.
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From 50833daba0b1dbe2ed364b1e980b67a09a312789 Mon Sep 17 00:00:00 2001
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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 | 60 +++++++++++++++++++++++++++++++++++++++++------------
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1 file changed, 47 insertions(+), 13 deletions(-)
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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..7a3805e 100644
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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 +9,12 @@ project('freebayes', ['cpp', 'c'],
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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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@ -23,10 +23,11 @@ index f6bf242..7a3805e 100644
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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 +63,41 @@ else
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@@ -59,6 +64,56 @@ else
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]
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endif
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@ -42,11 +43,26 @@ index f6bf242..7a3805e 100644
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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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@ -68,17 +84,18 @@ index f6bf242..7a3805e 100644
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#
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@@ -105,22 +144,17 @@ seqlib_src = [
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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/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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@ -90,37 +107,43 @@ index f6bf242..7a3805e 100644
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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/split.cpp',
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+ vcflib_src,
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'src/LeftAlign.cpp',
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]
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@@ -135,8 +169,8 @@ incdir = include_directories(
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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/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/multichoose',
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'vcflib/filevercmp')
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+ vcflib_includes)
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@@ -152,7 +186,7 @@ executable('freebayes',
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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, 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 +199,7 @@ executable('bamleftalign',
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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, 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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