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-rw-r--r--gn/packages/bioinformatics.scm167
1 files changed, 167 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index ea4bf91..ffa28ae 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -20,6 +20,7 @@
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages databases)
+ #:use-module (gnu packages cmake)
#:use-module (gnu packages cpio)
#:use-module (gnu packages file)
#:use-module (gnu packages gcc)
@@ -48,6 +49,172 @@
#:use-module (gn packages statistics)
#:use-module (srfi srfi-1))
+(define-public freebayes
+ (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
+ (package
+ (name "freebayes")
+ (version (string-append "v1.0.2-" (string-take commit 7)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/freebayes.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("cmake" ,cmake)
+ ("htslib" ,htslib)
+ ("zlib" ,zlib)
+ ("python" ,python-2)
+ ("perl" ,perl)
+ ("bamtools-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ekg/bamtools/archive/"
+ "e77a43f5097ea7eee432ee765049c6b246d49baa" ".tar.gz"))
+ (file-name "bamtools-src.tar.gz")
+ (sha256
+ (base32 "0rqymka21g6lfjfgxzr40pxz4c4fcl77jpy1np1li70pnc7h2cs1"))))
+ ("vcflib-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/vcflib/vcflib/archive/"
+ "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92" ".tar.gz"))
+ (file-name "vcflib-5ac0913.tar.gz")
+ (sha256
+ (base32 "0ywshwpif059z5h0g7zzrdfzzdj2gr8xvwlwcsdxrms3p9iy35h8"))))
+ ;; These are submodules for the vcflib version used in freebayes
+ ("tabixpp-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ekg/tabixpp/archive/"
+ "bbc63a49acc52212199f92e9e3b8fba0a593e3f7" ".tar.gz"))
+ (file-name "tabixpp-src.tar.gz")
+ (sha256
+ (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77"))))
+ ("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"))))
+ ("smithwaterman-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ekg/smithwaterman/archive/"
+ "203218b47d45ac56ef234716f1bd4c741b289be1" ".tar.gz"))
+ (file-name "smithwaterman-src.tar.gz")
+ (sha256
+ (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b"))))
+ ("multichoose-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ekg/multichoose/archive/"
+ "73d35daa18bf35729b9ba758041a9247a72484a5" ".tar.gz"))
+ (file-name "multichoose-src.tar.gz")
+ (sha256
+ (base32 "07aizwdabmlnjaq4p3v0vsasgz1xzxid8xcxcw3paq8kh9c1099i"))))
+ ("fsom-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ekg/fsom/archive/"
+ "a6ef318fbd347c53189384aef7f670c0e6ce89a3" ".tar.gz"))
+ (file-name "fsom-src.tar.gz")
+ (sha256
+ (base32 "0q6b57ppxfvsm5cqmmbfmjpn5qvx2zi5pamvp3yh8gpmmz8cfbl3"))))
+ ("filevercmp-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ekg/filevercmp/archive/"
+ "1a9b779b93d0b244040274794d402106907b71b7" ".tar.gz"))
+ (file-name "filevercmp-src.tar.gz")
+ (sha256
+ (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
+ ("fastahack-src"
+ ,(origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ekg/fastahack/archive/"
+ "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd" ".tar.gz"))
+ (file-name "fastahack-src.tar.gz")
+ (sha256
+ (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2"))))
+ ))
+ (arguments
+ `(#:tests? #f
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'check)
+ (add-after 'unpack 'unpack-submodule-sources
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((unpack (lambda (source target)
+ (with-directory-excursion target
+ (zero? (system* "tar" "xvf"
+ (assoc-ref inputs source)
+ "--strip-components=1"))))))
+ (and
+ (unpack "bamtools-src" "bamtools")
+ (unpack "vcflib-src" "vcflib")
+ (unpack "intervaltree-src" "intervaltree")
+ (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")))))
+ (add-after 'unpack-submodule-sources 'fix-makefile
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* '("vcflib/Makefile")
+ (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0"))))
+ (replace
+ 'build
+ (lambda* (#:key inputs make-flags #:allow-other-keys)
+ (and
+ ;; We must compile Bamtools before we can compile the main
+ ;; project.
+ (with-directory-excursion "bamtools"
+ (system* "mkdir" "build")
+ (with-directory-excursion "build"
+ (and (zero? (system* "cmake" "../"))
+ (zero? (system* "make")))))
+ ;; We must compile vcflib before we can compile the main
+ ;; project.
+ (with-directory-excursion "vcflib"
+ (with-directory-excursion "tabixpp"
+ (zero? (system* "make")))
+ (zero? (system* "make" "CC=gcc"
+ (string-append "CFLAGS=\"" "-Itabixpp "
+ "-I" (assoc-ref inputs "htslib") "/include " "\"") "all")))
+
+ (with-directory-excursion "src"
+ (zero? (system* "make"))))))
+ (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))))
+ ;; (replace
+ ;; 'check
+ ;; (lambda* (#:key outputs #:allow-other-keys)
+ ;; (with-directory-excursion "test"
+ ;; (zero? (system* "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:non-copyleft))))
+
(define-public r-biocpreprocesscore
(package
(name "r-biocpreprocesscore")