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author | Ricardo Wurmus <rekado@elephly.net> | 2021-04-23 15:52:36 +0200 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2021-04-23 15:53:51 +0200 |
commit | f1f17c7bba778ec03a5e40a34591564684461df5 (patch) | |
tree | 97a1cd98ed5c9e0e046a95239d7a9092920830cf /gnu | |
parent | a9b01b758213fe5854f305ebc767cde01794f6c6 (diff) | |
download | guix-patches-f1f17c7bba778ec03a5e40a34591564684461df5.tar guix-patches-f1f17c7bba778ec03a5e40a34591564684461df5.tar.gz |
gnu: Add shorah.
* gnu/packages/bioinformatics.scm (shorah): New variable.
Diffstat (limited to 'gnu')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 58 |
1 files changed, 58 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a3dd76c3bd..0aaf30872e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7601,6 +7601,64 @@ Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.") (license license:gpl3+))) +(define-public shorah + (package + (name "shorah") + (version "1.99.2") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/cbg-ethz/shorah" + "/releases/download/v" version + "/shorah-" version ".tar.xz")) + (sha256 + (base32 + "158dir9qcqspknlnyfr9zwk41x48nrh5wcg10k2grh9cidp9daiq")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-test-wrapper + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (substitute* "examples/run_end2end_test" + (("\\$\\{interpreter\\} ../\\$\\{testscript\\}") + (string-append bin "/${testscript}")))))) + (delete 'check) + (add-after 'install 'wrap-programs + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (site (string-append + out "/lib/python" + ,(version-major+minor + (package-version python)) + "/site-packages")) + (pythonpath (getenv "PYTHONPATH")) + (script (string-append out "/bin/shorah"))) + (chmod script #o555) + (wrap-program script `("PYTHONPATH" ":" prefix (,site ,pythonpath)))))) + (add-after 'wrap-programs 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "make" "check"))))))) + (inputs + `(("boost" ,boost) + ("htslib" ,htslib) + ("python" ,python) + ("python-biopython" ,python-biopython) + ("python-numpy" ,python-numpy) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "") + (synopsis "Short reads assembly into haplotypes") + (description + "ShoRAH is a project for the analysis of next generation sequencing data. +It is designed to analyse genetically heterogeneous samples. Its tools +provide error correction, haplotype reconstruction and estimation of the +frequency of the different genetic variants present in a mixed sample.") + (license license:gpl3+))) + (define-public ruby-bio-kseq (package (name "ruby-bio-kseq") |