diff options
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 16 | ||||
| -rw-r--r-- | gnu/packages/patches/freebayes-devendor-deps.patch | 152 |
3 files changed, 7 insertions, 162 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 1c692e0ce4..153f6ee8d7 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1019,7 +1019,6 @@ dist_patch_DATA = \ %D%/packages/patches/fpc-reproducibility.patch \ %D%/packages/patches/fplll-std-fenv.patch \ %D%/packages/patches/freedink-engine-fix-sdl-hints.patch \ - %D%/packages/patches/freebayes-devendor-deps.patch \ %D%/packages/patches/freeimage-unbundle.patch \ %D%/packages/patches/fuse-overlapping-headers.patch \ %D%/packages/patches/gajim-honour-GAJIM_PLUGIN_PATH.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2de8a59d3c..1e38c6e0e7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13572,7 +13572,7 @@ manipulations on VCF files.") (define-public freebayes (package (name "freebayes") - (version "1.3.3") + (version "1.3.5") (source (origin (method git-fetch) (uri (git-reference @@ -13580,8 +13580,7 @@ manipulations on VCF files.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0myz3giad7jqp6ricdfnig9ymlcps2h67mlivadvx97ngagm85z8")) - (patches (search-patches "freebayes-devendor-deps.patch")) + (base32 "1l0z88gq57kva677a6xri5g9k2d9h9lk5yk1q2xmq64wqhv7dvc3")) (modules '((guix build utils))) (snippet '(begin @@ -13593,8 +13592,7 @@ manipulations on VCF files.") ("htslib" ,htslib) ("smithwaterman" ,smithwaterman) ("tabixpp" ,tabixpp) - ("vcflib" ,vcflib) - ("zlib" ,zlib))) + ("vcflib" ,vcflib))) (native-inputs `(("bash-tap" ,bash-tap) ("bc" ,bc) @@ -13627,13 +13625,13 @@ manipulations on VCF files.") (string-append bash-tap "/bin/bash-tap-bootstrap")) (("source.*bash-tap-bootstrap") (string-append "source " bash-tap "/bin/bash-tap-bootstrap"))) - (substitute* "meson.build" - ;; Some inputs aren't actually needed. - ((".*bamtools/src.*") "") - ((".*multichoose.*") "")) (substitute* '("src/BedReader.cpp" "src/BedReader.h") (("../intervaltree/IntervalTree.h") "IntervalTree.h")) + (substitute* "meson.build" + ;; Our pkg-config file is vcflib.pc + (("libvcflib") "vcflib") + (("vcflib_inc,") "")) #t))) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs #:allow-other-keys) 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 - |