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-rw-r--r--gn/packages/bioinformatics.scm181
1 files changed, 180 insertions, 1 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index d37a287..295a2b3 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -49,6 +49,56 @@
#:use-module (gn packages statistics)
#:use-module (srfi srfi-1))
+(define-public freec
+ (package
+ (name "control-freec")
+ (version "8.7")
+ (source (origin
+ (method url-fetch)
+ (uri "http://bioinfo-out.curie.fr/projects/freec/src/FREEC_Linux64.tar.gz")
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "12sl7gxbklhvv0687qjhml1z4lwpcn159zcyxvawvclsrzqjmv0h"))))
+ (build-system gnu-build-system)
+ ;; The source code's filename indicates only a 64-bit Linux build.
+ ;; We need to investigate whether this is true.
+ (supported-systems '("x86_64-linux"))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ ;; There's no configure phase because there are no external
+ ;; dependencies.
+ (delete 'configure)
+ ;; There are no tests.
+ (delete 'check)
+ (replace
+ 'unpack
+ (lambda* (#:key source #:allow-other-keys)
+ (and
+ (zero? (system* "mkdir" "source"))
+ (with-directory-excursion "source"
+ (zero? (system* "tar" "xvf" source))))))
+ (replace
+ 'build
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "source"
+ (zero? (system* "make")))))
+ (replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "source/freec" bin)))))))
+ (home-page "http://bioinfo-out.curie.fr/projects/freec/")
+ (synopsis "Tool for detection of copy-number changes and allelic imbalances
+(including LOH) using deep-sequencing data")
+ (description "Control-FREEC automatically computes, normalizes, segments
+copy number and beta allele frequency (BAF) profiles, then calls copy number
+alterations and LOH. The control (matched normal) sample is optional for whole
+genome sequencing data but mandatory for whole exome or targeted sequencing
+data. For whole genome sequencing data analysis, the program can also use
+mappability data (files created by GEM). ")
+ (license license:gpl2+)))
+
(define-public freebayes
(let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
(package
@@ -213,7 +263,7 @@ 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))))
+ (license license:expat))))
(define-public r-biocpreprocesscore
(package
@@ -614,3 +664,132 @@ supported.")
(description
"FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.")
(license license:gpl3+)))
+
+(define-public vcflib
+ (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
+ (package
+ (name "vcflib")
+ (version (string-append "v1.0.2-" (string-take commit 7)))
+ (source
+ (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"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("htslib" ,htslib)
+ ("zlib" ,zlib)
+ ("python" ,python-2)
+ ("perl" ,perl)
+ ("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 "intervaltree-src" "intervaltree")
+ (unpack "fastahack-src" "fastahack")
+ (unpack "filevercmp-src" "filevercmp")
+ (unpack "fsom-src" "fsom")
+ (unpack "intervaltree-src" "intervaltree")
+ (unpack "multichoose-src" "multichoose")
+ (unpack "smithwaterman-src" "smithwaterman")
+ (unpack "tabixpp-src" "tabixpp")))))
+ (add-after 'unpack-submodule-sources 'fix-makefile
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* '("Makefile")
+ (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0"))))
+ (replace
+ 'build
+ (lambda* (#:key inputs make-flags #:allow-other-keys)
+ (with-directory-excursion "tabixpp"
+ (zero? (system* "make")))
+ (zero? (system* "make" "CC=gcc"
+ (string-append "CFLAGS=\"" "-Itabixpp "
+ "-I" (assoc-ref inputs "htslib") "/include " "\"") "all"))))
+ (replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+ (lib (string-append (assoc-ref outputs "out") "/lib")))
+ (for-each (lambda (file)
+ (install-file file bin))
+ (find-files "bin" ".*"))
+ (install-file "libvcflib.a" lib)))))))
+ (home-page "https://github.com/vcflib/vcflib/")
+ (synopsis "Library for parsing and manipulating VCF files")
+ (description "Vcflib provides methods to manipulate and interpret
+sequence variation as it can be described by VCF. It is both an API for parsing
+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))))
+