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04/04: gnu: freebayes: Update to 1.3.3.
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From: |
guix-commits |
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Subject: |
04/04: gnu: freebayes: Update to 1.3.3. |
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Date: |
Sun, 17 Jan 2021 08:48:01 -0500 (EST) |
efraim pushed a commit to branch master
in repository guix.
commit fc9fd5496f33f697f4dc1e0dc1f20ba62c15726a
Author: Efraim Flashner <efraim@flashner.co.il>
AuthorDate: Sun Jan 17 15:31:21 2021 +0200
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.
---
gnu/local.mk | 1 +
gnu/packages/bioinformatics.scm | 203 +++++++++------------
gnu/packages/patches/freebayes-devendor-deps.patch | 129 +++++++++++++
3 files changed, 218 insertions(+), 115 deletions(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index 77f1d4a..6f66021 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -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 \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7326686..c527111 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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
diff --git a/gnu/packages/patches/freebayes-devendor-deps.patch
b/gnu/packages/patches/freebayes-devendor-deps.patch
new file mode 100644
index 0000000..580f53a
--- /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
+