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gnu: hisat2: Update to 2.2.1.

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* gnu/packages/bioinformatics.scm (hisat2): Update to 2.2.1.
[source]: Fetch from git repository on Github.
[arguments]: Add phase to build manual; remove trailing #t from other phases.
[native-inputs]: Remove unzip.
[home-page]: Update.
[inputs]: Add python-wrapper.
This commit is contained in:
Ricardo Wurmus 2021-03-16 11:03:58 +01:00
parent 097cf21d1d
commit fcf8c6c565
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GPG key ID: 197A5888235FACAC
1 changed files with 17 additions and 12 deletions
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@ -3819,15 +3819,17 @@ particular, reads spanning multiple exons.")
(define-public hisat2 (define-public hisat2
(package (package
(name "hisat2") (name "hisat2")
(version "2.0.5") (version "2.2.1")
(source (source
(origin (origin
(method url-fetch) (method git-fetch)
(uri (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2" (uri (git-reference
"/downloads/hisat2-" version "-source.zip")) (url "https://github.com/DaehwanKimLab/hisat2/")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g")))) "0lmzdhzjkvxw7n5w40pbv5fgzd4cz0f9pxczswn3d4cr0k10k754"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; no check target `(#:tests? #f ; no check target
@ -3840,9 +3842,12 @@ particular, reads spanning multiple exons.")
(add-after 'unpack 'make-deterministic (add-after 'unpack 'make-deterministic
(lambda _ (lambda _
(substitute* "Makefile" (substitute* "Makefile"
(("`date`") "0")) (("`date`") "0"))))
#t))
(delete 'configure) (delete 'configure)
(add-before 'build 'build-manual
(lambda _
(mkdir-p "doc")
(invoke "make" "doc")))
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")) (let* ((out (assoc-ref outputs "out"))
@ -3853,13 +3858,13 @@ particular, reads spanning multiple exons.")
(find-files "." (find-files "."
"hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")) "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))
(mkdir-p doc) (mkdir-p doc)
(install-file "doc/manual.inc.html" doc)) (install-file "doc/manual.inc.html" doc)))))))
#t)))))
(native-inputs (native-inputs
`(("unzip" ,unzip) ; needed for archive from ftp `(("perl" ,perl)
("perl" ,perl)
("pandoc" ,pandoc))) ; for documentation ("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") (synopsis "Graph-based alignment of genomic sequencing reads")
(description "HISAT2 is a fast and sensitive alignment program for mapping (description "HISAT2 is a fast and sensitive alignment program for mapping
next-generation sequencing reads (both DNA and RNA) to a population of human next-generation sequencing reads (both DNA and RNA) to a population of human