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-rw-r--r--gnu/packages/bioinformatics.scm39
1 files changed, 39 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4fd9459350..7fc6af3c4e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1386,6 +1386,45 @@ sequences.")
;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
(license license:gpl3+)))
+(define-public subread
+ (package
+ (name "subread")
+ (version "1.4.6-p2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "mirror://sourceforge/subread/subread-"
+ version "-source.tar.gz"))
+ (sha256
+ (base32
+ "06sv9mpcsdj6p68y15d6gi70lca3lxmzk0dn61hg0kfsa7rxmsr3"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ;no "check" target
+ #:make-flags '("-f" "Makefile.Linux")
+ #:phases
+ (alist-cons-after
+ 'unpack 'enter-dir
+ (lambda _ (chdir "src") #t)
+ (alist-replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (mkdir-p bin)
+ (copy-recursively "../bin" bin)))
+ ;; no "configure" script
+ (alist-delete 'configure %standard-phases)))))
+ (inputs `(("zlib" ,zlib)))
+ (home-page "http://bioinf.wehi.edu.au/subread-package/")
+ (synopsis "Tool kit for processing next-gen sequencing data")
+ (description
+ "The subread package contains the following tools: subread aligner, a
+general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
+and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
+features; exactSNP: a SNP caller that discovers SNPs by testing signals
+against local background noises.")
+ (license license:gpl3+)))
+
(define-public shogun
(package
(name "shogun")