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authorEfraim Flashner <efraim@flashner.co.il>2021-06-06 12:07:01 +0300
committerEfraim Flashner <efraim@flashner.co.il>2021-06-06 12:13:28 +0300
commitb65c02e2d35af6fbe1d1810d6c69cfab194e13e2 (patch)
tree6520661034bfe629017ad4ffca7e554b9a46dd0c /gnu/packages/patches
parent1fd8819fac313d99c06f07477076be2d66e06a92 (diff)
gnu: freebayes: Update to 1.3.5.
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5. [source]: Remove patch. [arguments]: Adjust custom 'patch-source phase for changes in source. [inputs]: Remove zlib. * gnu/packages/patches/freebayes-devendor-deps.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
Diffstat (limited to 'gnu/packages/patches')
-rw-r--r--gnu/packages/patches/freebayes-devendor-deps.patch152
1 files changed, 0 insertions, 152 deletions
diff --git a/gnu/packages/patches/freebayes-devendor-deps.patch b/gnu/packages/patches/freebayes-devendor-deps.patch
deleted file mode 100644
index 9886de11fb..0000000000
--- a/gnu/packages/patches/freebayes-devendor-deps.patch
+++ /dev/null
@@ -1,152 +0,0 @@
-This patch is original to Guix, ongoing work to upstream bits as possible.
-
-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 | 84 +++++++++++++++++++++++++++++++++++++++++------------
- 1 file changed, 66 insertions(+), 18 deletions(-)
-
-diff --git a/meson.build b/meson.build
-index f6bf242..bded4af 100644
---- a/meson.build
-+++ b/meson.build
-@@ -9,8 +9,13 @@ project('freebayes', ['cpp', 'c'],
-
- zlib_dep = dependency('zlib')
- lzma_dep = dependency('liblzma')
-+simde_dep = dependency('simde')
- bzip2_dep = dependency('bz2lib', required: false)
- htslib_dep = dependency('htslib', required : false)
-+tabixpp_dep = dependency('tabixpp', required : false)
-+fastahack_dep = dependency('fastahack', required : false)
-+smithwaterman_dep = dependency('smithwaterman', required : false)
-+vcflib_dep = dependency('vcflib', required: false)
- thread_dep = dependency('threads')
-
- if htslib_dep.found()
-@@ -59,6 +64,56 @@ else
- ]
- endif
-
-+if tabixpp_dep.found()
-+ tabixpp_includes = ''
-+ tabixpp_src = []
-+else
-+ tabixpp_includes = [
-+ 'vcflib/tabixpp',
-+ ]
-+ tabixpp_src = [
-+ 'vcflib/tabixpp/tabix.cpp',
-+ ]
-+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
-+
-+if smithwaterman_dep.found()
-+ smithwaterman_includes = ''
-+ smithwaterman_src = []
-+else
-+ smithwaterman_includes = [
-+ 'vcflib/smithwaterman',
-+ ]
-+ smithwaterman_src = [
-+ 'vcflib/smithwaterman/SmithWatermanGotoh.cpp',
-+ 'vcflib/smithwaterman/disorder.cpp',
-+ 'vcflib/smithwaterman/Repeats.cpp',
-+ 'vcflib/smithwaterman/LeftAlign.cpp',
-+ 'vcflib/smithwaterman/IndelAllele.cpp',
-+ ]
-+endif
-
-
- #
-@@ -105,23 +160,18 @@ seqlib_src = [
- ]
-
- vcflib_src = [
-- 'vcflib/tabixpp/tabix.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,
- ]
-
- bamleftalign_src = [
- 'src/bamleftalign.cpp',
- 'src/IndelAllele.cpp',
- 'contrib/SeqLib/src/BamWriter.cpp',
-- 'vcflib/fastahack/Fasta.cpp',
-- 'vcflib/smithwaterman/LeftAlign.cpp',
-- 'vcflib/smithwaterman/IndelAllele.cpp',
-- 'vcflib/src/split.cpp',
-+ fastahack_src,
-+ smithwaterman_src,
-+ vcflib_src,
- 'src/LeftAlign.cpp',
- ]
-
-@@ -134,11 +184,9 @@ incdir = include_directories(
- 'ttmath',
- 'contrib',
- 'contrib/SeqLib',
-- 'vcflib/src',
-- 'vcflib/tabixpp',
-- 'vcflib/smithwaterman',
-- 'vcflib/multichoose',
-- 'vcflib/filevercmp')
-+ tabixpp_includes,
-+ smithwaterman_includes,
-+ vcflib_includes)
-
- 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, vcflib_dep, thread_dep],
- install: true
- )
-
-@@ -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, vcflib_dep, thread_dep],
- install: true
- )
-
---
-2.30.0
-