diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2021-03-16 11:03:58 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-03-16 11:12:01 +0100 |
| commit | fcf8c6c5652cac87647d87e87dede3a7b154716b (patch) | |
| tree | b17f6d34b46cf8a95fec0bda9e993dc9fc2c221d /gnu | |
| parent | 097cf21d1d34f4f66a403c3fb6e15b6709c4dd8a (diff) | |
gnu: hisat2: Update to 2.2.1.
* 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.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 29 |
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 |