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-rw-r--r--gnu/packages/bioinformatics.scm66
1 files changed, 65 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c0d14388e1..9219bc2975 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -29,8 +29,9 @@
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
- #:use-module (gnu packages python))
+ #:use-module (gnu packages python)
#:use-module (gnu packages tbb)
+ #:use-module (gnu packages zip))
(define-public bedtools
(package
@@ -181,6 +182,69 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from
Illumina, Roche 454, and the SOLiD platform.")
(license license:gpl3)))
+(define-public hisat
+ (package
+ (name "hisat")
+ (version "0.1.4")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
+ version "-beta-source.zip"))
+ (sha256
+ (base32
+ "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ;no check target
+ #:make-flags '("allall")
+ #:phases
+ (alist-replace
+ 'unpack
+ (lambda* (#:key source #:allow-other-keys)
+ (and (zero? (system* "unzip" source))
+ (chdir "hisat-0.1.4-beta")))
+ (alist-cons-after
+ 'unpack 'patch-sources
+ (lambda _
+ ;; XXX Cannot use snippet because zip files are not supported
+ (substitute* "Makefile"
+ (("^CC = .*$") "CC = gcc")
+ (("^CPP = .*$") "CPP = g++")
+ ;; replace BUILD_HOST and BUILD_TIME for deterministic build
+ (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
+ (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
+ (substitute* '("hisat-build" "hisat-inspect")
+ (("/usr/bin/env") (which "env"))))
+ (alist-replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (mkdir-p bin)
+ (for-each
+ (lambda (file)
+ (copy-file file (string-append bin file)))
+ (find-files
+ "."
+ "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))
+ (alist-delete 'configure %standard-phases))))))
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (inputs
+ `(("perl" ,perl)
+ ("python" ,python)
+ ("zlib" ,zlib)))
+ (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
+ (synopsis "Hierarchical indexing for spliced alignment of transcripts")
+ (description
+ "HISAT is a fast and sensitive spliced alignment program for mapping
+RNA-seq reads. In addition to one global FM index that represents a whole
+genome, HISAT uses a large set of small FM indexes that collectively cover the
+whole genome. These small indexes (called local indexes) combined with
+several alignment strategies enable effective alignment of RNA-seq reads, in
+particular, reads spanning multiple exons.")
+ (license license:gpl3+)))
+
(define-public samtools
(package
(name "samtools")