Package: guix-patches;
Reported by: Pierre Neidhardt <mail <at> ambrevar.xyz>
Date: Sat, 18 May 2019 17:26:01 UTC
Severity: normal
Tags: patch
Done: Efraim Flashner <efraim <at> flashner.co.il>
Bug is archived. No further changes may be made.
View this message in rfc822 format
From: Pierre Neidhardt <mail <at> ambrevar.xyz> To: 35792 <at> debbugs.gnu.org Subject: [bug#35792] [PATCH 7/7] gnu: Add freebayes. Date: Sat, 18 May 2019 19:26:40 +0200
* gnu/packages/bioinformatics.scm (freebayes): New variable.
---
gnu/packages/bioinformatics.scm | 127 ++++++++++++++++++++++++++++++++
1 file changed, 127 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 665c807de9..704db184eb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15103,3 +15103,130 @@ and operating on records of genomic variation as it can be described by the VCF
format, and a collection of command-line utilities for executing complex
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.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("zlib" ,zlib)
+ ("htslib" ,htslib)))
+ (native-inputs
+ `(("bc" ,bc) ; Needed for running tests.
+ ("samtools" ,samtools) ; Needed for running tests.
+ ("parallel" ,parallel) ; Needed for running tests.
+ ("procps" ,procps) ; Needed for running tests.
+ ("bamtools" ,bamtools)
+ ("bamtools" ,bamtools)
+ ("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-freebayes))
+ ("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"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/ekg/intervaltree/archive/"
+ "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz"))
+ (file-name "intervaltree-src.tar.gz")
+ (sha256
+ (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks"))))
+ ;; 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.tar.gz")
+ (sha256
+ (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga"))))))
+ (arguments
+ `(#:tests? #f ; TODO: Re-enable when we have grep with perl support.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (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-makefile
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; We don't have the .git folder to get the version tag from.
+ (substitute* '("vcflib/Makefile")
+ (("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version)))))
+ (replace 'build
+ (lambda* (#:key inputs make-flags #:allow-other-keys)
+ (with-directory-excursion "vcflib"
+ (with-directory-excursion "tabixpp"
+ (pk "Compile tabixpp before compiling the main project.")
+ (let ((htslib-ref (assoc-ref inputs "htslib")))
+ (invoke "make" "HTS_HEADERS="
+ (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
+ (string-append "LIBPATH=-L. -L" htslib-ref "/include"))))
+ (pk "Compile vcflib before compiling the main project.")
+ (invoke "make" "CC=gcc"
+ (string-append "CFLAGS=\"" "-Itabixpp "
+ "-I" (assoc-ref inputs "htslib") "/include " "\"")
+ "all"))
+ (pk "Compile the main project.")
+ (with-directory-excursion "src"
+ (substitute* "Makefile"
+ (("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools"))
+ (invoke "make"
+ (string-append "BAMTOOLS_ROOT="
+ (assoc-ref inputs "bamtools"))))))
+ (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))))
+ ;; TODO: There are three tests that fail. All because of the -P
+ ;; (--perl-regexp) option in grep, which is not compiled into the
+ ;; version of grep in Guix.
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "make" "test")))))))
+ (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))))
--
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1994-97 Ian Jackson.