mirror of
https://codeberg.org/guix/guix.git
synced 2025-10-02 02:15:12 +00:00
fc9fd5496f
* 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.
129 lines
3.5 KiB
Diff
129 lines
3.5 KiB
Diff
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
|
|
|