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gnu: freebayes: Update to 1.3.3.

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* 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.
This commit is contained in:
Efraim Flashner 2021-01-17 15:31:21 +02:00
parent 3ddeefe854
commit fc9fd5496f
No known key found for this signature in database
GPG key ID: 41AAE7DCCA3D8351
3 changed files with 218 additions and 115 deletions
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1
gnu/local.mk
View file

@ -998,6 +998,7 @@ 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 \

203
gnu/packages/bioinformatics.scm
View file

@ -57,6 +57,7 @@
#:use-module (guix build-system trivial)
#:use-module (guix deprecation)
#:use-module (gnu packages)
#:use-module (gnu packages assembly)
#:use-module (gnu packages autotools)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
@ -15011,125 +15012,97 @@ manipulations on VCF files.")
(license license:expat)))
(define-public freebayes
(let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")
(revision "1")
(version "1.0.2"))
(package
(name "freebayes")
(version (git-version version revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ekg/freebayes")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2"))))
(build-system gnu-build-system)
(inputs
`(("bamtools" ,bamtools)
("htslib" ,htslib)
("zlib" ,zlib)))
(native-inputs
`(("bc" ,bc) ; Needed for running tests.
("samtools" ,samtools) ; Needed for running tests.
("parallel" ,parallel) ; Needed for running tests.
("perl" ,perl) ; Needed for running tests.
("procps" ,procps) ; Needed for running tests.
("python" ,python-2) ; Needed for running tests.
("vcflib-src" ,(package-source vcflib))
;; These are submodules for the vcflib version used in freebayes.
;; This package builds against the .o files so we need to extract the source.
("tabixpp-src" ,(package-source tabixpp))
("smithwaterman-src" ,(package-source smithwaterman))
("multichoose-src" ,(package-source multichoose))
("fsom-src" ,(package-source fsom))
("filevercmp-src" ,(package-source filevercmp))
("fastahack-src" ,(package-source fastahack))
("intervaltree-src" ,(package-source intervaltree))
;; These submodules are needed to run the tests.
("bash-tap-src" ,(package-source bash-tap))
("test-simple-bash-src"
,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ingydotnet/test-simple-bash/")
(commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc")))
(file-name "test-simple-bash-src-checkout")
(sha256
(base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
(arguments
`(#:make-flags
(list "CC=gcc"
(string-append "BAMTOOLS_ROOT="
(assoc-ref %build-inputs "bamtools")))
#:test-target "test"
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-after 'unpack 'fix-tests
(lambda _
(substitute* "test/t/01_call_variants.t"
(("grep -P \"\\(\\\\t500\\$\\|\\\\t11000\\$\\|\\\\t1000\\$\\)\"")
"grep -E ' (500|11000|1000)$'"))
#t))
(add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs #:allow-other-keys)
(let ((unpack (lambda (source target)
(with-directory-excursion target
(if (file-is-directory? (assoc-ref inputs source))
(copy-recursively (assoc-ref inputs source) ".")
(invoke "tar" "xvf"
(assoc-ref inputs source)
"--strip-components=1"))))))
(and
(unpack "vcflib-src" "vcflib")
(unpack "fastahack-src" "vcflib/fastahack")
(unpack "filevercmp-src" "vcflib/filevercmp")
(unpack "fsom-src" "vcflib/fsom")
(unpack "intervaltree-src" "vcflib/intervaltree")
(unpack "multichoose-src" "vcflib/multichoose")
(unpack "smithwaterman-src" "vcflib/smithwaterman")
(unpack "tabixpp-src" "vcflib/tabixpp")
(unpack "test-simple-bash-src" "test/test-simple-bash")
(unpack "bash-tap-src" "test/bash-tap")))))
(add-after 'unpack-submodule-sources 'fix-makefiles
(lambda _
;; We don't have the .git folder to get the version tag from.
(substitute* "vcflib/Makefile"
(("^GIT_VERSION.*")
(string-append "GIT_VERSION = v" ,version)))
(substitute* "src/Makefile"
(("-I\\$\\(BAMTOOLS_ROOT\\)/src")
"-I$(BAMTOOLS_ROOT)/include/bamtools"))
#t))
(add-before 'build 'build-tabixpp-and-vcflib
(lambda* (#:key inputs make-flags #:allow-other-keys)
(with-directory-excursion "vcflib"
(with-directory-excursion "tabixpp"
(apply invoke "make"
(string-append "HTS_LIB="
(assoc-ref inputs "htslib")
"/lib/libhts.a")
make-flags))
(apply invoke "make"
(string-append "CFLAGS=-Itabixpp")
"all"
make-flags))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "bin/freebayes" bin)
(install-file "bin/bamleftalign" bin))
#t)))))
(home-page "https://github.com/ekg/freebayes")
(synopsis "Haplotype-based variant detector")
(description "FreeBayes is a Bayesian genetic variant detector designed to
(package
(name "freebayes")
(version "1.3.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ekg/freebayes")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0myz3giad7jqp6ricdfnig9ymlcps2h67mlivadvx97ngagm85z8"))
(patches (search-patches "freebayes-devendor-deps.patch"))
(modules '((guix build utils)))
(snippet
'(begin
(delete-file-recursively "contrib/htslib")
#t))))
(build-system meson-build-system)
(inputs
`(("fastahack" ,fastahack)
("htslib" ,htslib)
("smithwaterman" ,smithwaterman)
("tabixpp" ,tabixpp)
("zlib" ,zlib)))
(native-inputs
`(("bash-tap" ,bash-tap)
("bc" ,bc)
("grep" ,grep) ; Built with perl support.
("parallel" ,parallel)
("perl" ,perl)
("pkg-config" ,pkg-config)
("samtools" ,samtools)
("simde" ,simde)
;; We need some binaries from vcflib, but we also need to link against a
;; subset of the library. Vendor the parts we need until we have a shared library.
("vcflib" ,vcflib)
("vcflib-src" ,(package-source vcflib))
("intervaltree-src" ,(package-source intervaltree))
;; This submodule is needed to run the tests.
("test-simple-bash-src"
,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ingydotnet/test-simple-bash/")
(commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc")))
(file-name "test-simple-bash-src-checkout")
(sha256
(base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-source
(lambda* (#:key inputs #:allow-other-keys)
(let ((bash-tap (assoc-ref inputs "bash-tap")))
(substitute* (find-files "test/t")
(("BASH_TAP_ROOT=bash-tap")
(string-append "BASH_TAP_ROOT=" bash-tap "/bin"))
(("bash-tap/bash-tap-bootstrap")
(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.*") "")
(("'vcflib/filevercmp'") ""))
#t)))
(add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs #:allow-other-keys)
(let ((unpack (lambda (source target)
(unless (directory-exists? target)
(mkdir-p target))
(with-directory-excursion target
(if (file-is-directory? (assoc-ref inputs source))
(copy-recursively (assoc-ref inputs source) ".")
(invoke "tar" "xvf"
(assoc-ref inputs source)
"--strip-components=1"))))))
(and
(unpack "vcflib-src" "vcflib")
(unpack "intervaltree-src" "vcflib/intervaltree")
(unpack "test-simple-bash-src" "test/test-simple-bash"))
#t))))))
(home-page "https://github.com/ekg/freebayes")
(synopsis "Haplotype-based variant detector")
(description "FreeBayes is a Bayesian genetic variant detector designed to
find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms),
indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and
complex events (composite insertion and substitution events) smaller than the
length of a short-read sequencing alignment.")
(license license:expat))))
(license license:expat)))
(define-public samblaster
(package

129
gnu/packages/patches/freebayes-devendor-deps.patch Normal file
View file

@ -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