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authorEfraim Flashner <efraim@flashner.co.il>2021-01-17 15:31:21 +0200
committerEfraim Flashner <efraim@flashner.co.il>2021-01-17 15:47:32 +0200
commitfc9fd5496f33f697f4dc1e0dc1f20ba62c15726a (patch)
tree4d398aab6234f711ad2bbbc5e2bc85105fec7763 /gnu/packages/patches
parent3ddeefe854a9f0fc3e33998f001e8445ee72a9f0 (diff)
gnu: freebayes: Update to 1.3.3.
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.3. [source]: Add patch. Add snippet to remove vendored library. [build-system]: Switch to meson-build-system. [inputs]: Remove bamtools. Add fastahack, smithwaterman, tabixpp. [native-inputs]: Remove procps, python-2, tabixpp source, smithwaterman source, multichoose source, fsom source, filevercmp source, fastahack source, bash-tap source. Add bash-tap, grep, pkg-config, simde, vcflib. [arguments]: Drop make-flags. Don't delete 'configure phase. Delete custom 'fix-tests, 'build-tabixpp-and-vcflib, 'fix-makefiles, 'install phases. Adjust 'unpack-submodule-sources phase to changed native-inputs. Add new 'patch-source phase.
Diffstat (limited to 'gnu/packages/patches')
-rw-r--r--gnu/packages/patches/freebayes-devendor-deps.patch129
1 files changed, 129 insertions, 0 deletions
diff --git a/gnu/packages/patches/freebayes-devendor-deps.patch b/gnu/packages/patches/freebayes-devendor-deps.patch
new file mode 100644
index 0000000000..580f53a3b1
--- /dev/null
+++ b/gnu/packages/patches/freebayes-devendor-deps.patch
@@ -0,0 +1,129 @@
+This patch is original to Guix, ongoing work to upstream bits as possible.
+
+From 50833daba0b1dbe2ed364b1e980b67a09a312789 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(-)
+
+diff --git a/meson.build b/meson.build
+index f6bf242..7a3805e 100644
+--- a/meson.build
++++ b/meson.build
+@@ -9,8 +9,12 @@ 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)
+ thread_dep = dependency('threads')
+
+ if htslib_dep.found()
+@@ -59,6 +63,41 @@ else
+ ]
+ endif
+
++if tabixpp_dep.found()
++ tabixpp_includes = ''
++ tabixpp_src = []
++else
++ tabixpp_includes = [
++ 'vcflib/tabixpp',
++ ]
++ tabixpp_src = [
++ 'vcflib/tabixpp/tabix.cpp',
++ ]
++endif
++
++if fastahack_dep.found()
++ fastahack_src = []
++else
++ fastahack_src = [
++ 'vcflib/fastahack/Fasta.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
+
+
+ #
+@@ -105,22 +144,17 @@ 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',
++ 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',
++ fastahack_src,
++ smithwaterman_src,
+ 'vcflib/src/split.cpp',
+ 'src/LeftAlign.cpp',
+ ]
+@@ -135,8 +169,8 @@ incdir = include_directories(
+ 'contrib',
+ 'contrib/SeqLib',
+ 'vcflib/src',
+- 'vcflib/tabixpp',
+- 'vcflib/smithwaterman',
++ tabixpp_includes,
++ smithwaterman_includes,
+ 'vcflib/multichoose',
+ 'vcflib/filevercmp')
+
+@@ -152,7 +186,7 @@ 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],
+ install: true
+ )
+
+@@ -165,7 +199,7 @@ 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],
+ install: true
+ )
+
+--
+2.30.0
+