diff options
Diffstat (limited to 'gnu/packages/patches/freebayes-devendor-deps.patch')
| -rw-r--r-- | gnu/packages/patches/freebayes-devendor-deps.patch | 152 |
1 files changed, 152 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..7e84666b85 --- /dev/null +++ b/gnu/packages/patches/freebayes-devendor-deps.patch @@ -0,0 +1,152 @@ +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('libvcflib', 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 + |