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-rw-r--r--gn/packages/bioinformatics.scm50
1 files changed, 50 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index d37a287..267d988 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