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Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 50 |
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 |