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-rw-r--r--gnu/packages/bioinformatics.scm29
1 files changed, 17 insertions, 12 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d9afe2c56f..90e81354a5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3819,15 +3819,17 @@ particular, reads spanning multiple exons.")
(define-public hisat2
(package
(name "hisat2")
- (version "2.0.5")
+ (version "2.2.1")
(source
(origin
- (method url-fetch)
- (uri (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2"
- "/downloads/hisat2-" version "-source.zip"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/DaehwanKimLab/hisat2/")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g"))))
+ "0lmzdhzjkvxw7n5w40pbv5fgzd4cz0f9pxczswn3d4cr0k10k754"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no check target
@@ -3840,9 +3842,12 @@ particular, reads spanning multiple exons.")
(add-after 'unpack 'make-deterministic
(lambda _
(substitute* "Makefile"
- (("`date`") "0"))
- #t))
+ (("`date`") "0"))))
(delete 'configure)
+ (add-before 'build 'build-manual
+ (lambda _
+ (mkdir-p "doc")
+ (invoke "make" "doc")))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@@ -3853,13 +3858,13 @@ particular, reads spanning multiple exons.")
(find-files "."
"hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))
(mkdir-p doc)
- (install-file "doc/manual.inc.html" doc))
- #t)))))
+ (install-file "doc/manual.inc.html" doc)))))))
(native-inputs
- `(("unzip" ,unzip) ; needed for archive from ftp
- ("perl" ,perl)
+ `(("perl" ,perl)
("pandoc" ,pandoc))) ; for documentation
- (home-page "https://ccb.jhu.edu/software/hisat2/index.shtml")
+ (inputs
+ `(("python" ,python-wrapper)))
+ (home-page "https://daehwankimlab.github.io/hisat2/")
(synopsis "Graph-based alignment of genomic sequencing reads")
(description "HISAT2 is a fast and sensitive alignment program for mapping
next-generation sequencing reads (both DNA and RNA) to a population of human