diff options
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 203 | ||||
| -rw-r--r-- | 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 77f1d4a096..6f66021c78 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 7326686245..c527111928 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 0000000000..580f53a3b1 --- /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 + |