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| author | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-02-18 15:00:04 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> | 2015-02-19 13:41:38 +0100 |
| commit | 8622a07280bc3c6f7b3f4a57fb496be8934f2a14 (patch) | |
| tree | b8f2731b0b5cbf113bb68fcb9c466451e6658774 | |
| parent | 04dec194d8e460831ec0695a944d9c7313affea2 (diff) | |
| download | guix-8622a07280bc3c6f7b3f4a57fb496be8934f2a14.tar.gz guix-8622a07280bc3c6f7b3f4a57fb496be8934f2a14.zip | |
gnu: Add RSeQC.
* gnu/packages/bioinformatics.scm (rseqc): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 44 |
1 files changed, 44 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5bd668ee14..c13e6499b7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -22,6 +22,7 @@ #:use-module (guix download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) + #:use-module (guix build-system python) #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages base) @@ -310,6 +311,49 @@ several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons.") (license license:gpl3+))) +(define-public rseqc + (package + (name "rseqc") + (version "2.6.1") + (source + (origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/rseqc/" + version "/RSeQC-" version ".tar.gz")) + (sha256 + (base32 "09rf0x9d6apjja5l01cgprj7vigpw6kiqhy34ibwwlxil0db0ri4")) + (modules '((guix build utils))) + (snippet + '(begin + ;; remove bundled copy of pysam + (delete-file-recursively "lib/pysam") + (substitute* "setup.py" + ;; remove dependency on outdated "distribute" module + (("^from distribute_setup import use_setuptools") "") + (("^use_setuptools\\(\\)") "") + ;; do not use bundled copy of pysam + (("^have_pysam = False") "have_pysam = True")))))) + (build-system python-build-system) + (arguments `(#:python ,python-2)) + (inputs + `(("python-cython" ,python2-cython) + ("python-pysam" ,python2-pysam) + ("python-numpy" ,python2-numpy) + ("python-setuptools" ,python2-setuptools) + ("zlib" ,zlib))) + (native-inputs + `(("python-nose" ,python2-nose))) + (home-page "http://rseqc.sourceforge.net/") + (synopsis "RNA-seq quality control package") + (description + "RSeQC provides a number of modules that can comprehensively evaluate +high throughput sequence data, especially RNA-seq data. Some basic modules +inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, +while RNA-seq specific modules evaluate sequencing saturation, mapped reads +distribution, coverage uniformity, strand specificity, etc.") + (license license:gpl3+))) + (define-public samtools (package (name "samtools") |