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authorEfraim Flashner <efraim@flashner.co.il>2021-01-19 11:38:06 +0200
committerEfraim Flashner <efraim@flashner.co.il>2021-01-19 11:41:07 +0200
commit99043adf46d3e27fb10939c1365552844596345d (patch)
treec0b73d9f3b454f9104cdb11a4097c092c14de818 /gnu/packages/patches/freebayes-devendor-deps.patch
parent1bbfe1789d07f8ae727a08b8386369ee736582cc (diff)
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.
Diffstat (limited to 'gnu/packages/patches/freebayes-devendor-deps.patch')
-rw-r--r--gnu/packages/patches/freebayes-devendor-deps.patch57
1 files changed, 40 insertions, 17 deletions
diff --git a/gnu/packages/patches/freebayes-devendor-deps.patch b/gnu/packages/patches/freebayes-devendor-deps.patch
index 580f53a3b1..7e84666b85 100644
--- a/gnu/packages/patches/freebayes-devendor-deps.patch
+++ b/gnu/packages/patches/freebayes-devendor-deps.patch
@@ -1,19 +1,19 @@
This patch is original to Guix, ongoing work to upstream bits as possible.
-From 50833daba0b1dbe2ed364b1e980b67a09a312789 Mon Sep 17 00:00:00 2001
+From 9acc56db5e7469f5976be38b52ba4993de98ee38 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 17 Jan 2021 13:27:17 +0200
Subject: [PATCH] devendor-dependants
---
- meson.build | 60 +++++++++++++++++++++++++++++++++++++++++------------
- 1 file changed, 47 insertions(+), 13 deletions(-)
+ meson.build | 84 +++++++++++++++++++++++++++++++++++++++++------------
+ 1 file changed, 66 insertions(+), 18 deletions(-)
diff --git a/meson.build b/meson.build
-index f6bf242..7a3805e 100644
+index f6bf242..bded4af 100644
--- a/meson.build
+++ b/meson.build
-@@ -9,8 +9,12 @@ project('freebayes', ['cpp', 'c'],
+@@ -9,8 +9,13 @@ project('freebayes', ['cpp', 'c'],
zlib_dep = dependency('zlib')
lzma_dep = dependency('liblzma')
@@ -23,10 +23,11 @@ index f6bf242..7a3805e 100644
+tabixpp_dep = dependency('tabixpp', required : false)
+fastahack_dep = dependency('fastahack', required : false)
+smithwaterman_dep = dependency('smithwaterman', required : false)
++vcflib_dep = dependency('libvcflib', required: false)
thread_dep = dependency('threads')
if htslib_dep.found()
-@@ -59,6 +63,41 @@ else
+@@ -59,6 +64,56 @@ else
]
endif
@@ -42,11 +43,26 @@ index f6bf242..7a3805e 100644
+ ]
+endif
+
++if vcflib_dep.found()
++ vcflib_includes = ''
++ vcflib_src = []
++else
++ vcflib_includes = [
++ 'vcflib/src',
++ 'vcflib/multichoose',
++ 'vcflib/filevercmp',
++ ]
++ vcflib_src = [
++ 'vcflib/src/Variant.cpp',
++ ]
++endif
++
+if fastahack_dep.found()
+ fastahack_src = []
+else
+ fastahack_src = [
+ 'vcflib/fastahack/Fasta.cpp',
++ 'vcflib/src/split.cpp',
+ ]
+endif
+
@@ -68,17 +84,18 @@ index f6bf242..7a3805e 100644
#
-@@ -105,22 +144,17 @@ seqlib_src = [
+@@ -105,23 +160,18 @@ seqlib_src = [
]
vcflib_src = [
- 'vcflib/tabixpp/tabix.cpp',
- 'vcflib/src/Variant.cpp',
+- 'vcflib/src/Variant.cpp',
- 'vcflib/smithwaterman/SmithWatermanGotoh.cpp',
- 'vcflib/smithwaterman/disorder.cpp',
- 'vcflib/smithwaterman/Repeats.cpp',
- 'vcflib/smithwaterman/LeftAlign.cpp',
- 'vcflib/smithwaterman/IndelAllele.cpp',
++ vcflib_src,
+ tabixpp_src,
+ smithwaterman_src,
]
@@ -90,37 +107,43 @@ index f6bf242..7a3805e 100644
- 'vcflib/fastahack/Fasta.cpp',
- 'vcflib/smithwaterman/LeftAlign.cpp',
- 'vcflib/smithwaterman/IndelAllele.cpp',
+- 'vcflib/src/split.cpp',
+ fastahack_src,
+ smithwaterman_src,
- 'vcflib/src/split.cpp',
++ vcflib_src,
'src/LeftAlign.cpp',
]
-@@ -135,8 +169,8 @@ incdir = include_directories(
+
+@@ -134,11 +184,9 @@ incdir = include_directories(
+ 'ttmath',
'contrib',
'contrib/SeqLib',
- 'vcflib/src',
+- 'vcflib/src',
- 'vcflib/tabixpp',
- 'vcflib/smithwaterman',
+- 'vcflib/multichoose',
+- 'vcflib/filevercmp')
+ tabixpp_includes,
+ smithwaterman_includes,
- 'vcflib/multichoose',
- 'vcflib/filevercmp')
++ vcflib_includes)
-@@ -152,7 +186,7 @@ executable('freebayes',
+ c_args = ['-fpermissive','-w']
+ cpp_args = ['-fpermissive','-w','-Wc++14-compat']
+@@ -152,7 +200,7 @@ executable('freebayes',
include_directories : incdir,
cpp_args : cpp_args,
c_args : c_args,
- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep],
-+ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, smithwaterman_dep, thread_dep],
++ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, smithwaterman_dep, vcflib_dep, thread_dep],
install: true
)
-@@ -165,7 +199,7 @@ executable('bamleftalign',
+@@ -165,7 +213,7 @@ executable('bamleftalign',
include_directories : incdir,
cpp_args : cpp_args,
c_args : c_args,
- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep],
-+ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, fastahack_dep, smithwaterman_dep, thread_dep],
++ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, fastahack_dep, smithwaterman_dep, vcflib_dep, thread_dep],
install: true
)