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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-02-18 15:00:04 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-02-19 13:41:38 +0100
commit8622a07280bc3c6f7b3f4a57fb496be8934f2a14 (patch)
treeb8f2731b0b5cbf113bb68fcb9c466451e6658774
parent04dec194d8e460831ec0695a944d9c7313affea2 (diff)
downloadguix-8622a07280bc3c6f7b3f4a57fb496be8934f2a14.tar.gz
guix-8622a07280bc3c6f7b3f4a57fb496be8934f2a14.zip
gnu: Add RSeQC.
* gnu/packages/bioinformatics.scm (rseqc): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm44
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+ ;; remove dependency on outdated "distribute" module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")