gnu: Add NGS SDK.
* gnu/packages/bioinformatics.scm (ngs-sdk): New variable.
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@ -1031,6 +1031,62 @@ variant calling (in conjunction with bcftools), and a simple alignment
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viewer.")
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(license license:expat)))
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(define-public ngs-sdk
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(package
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(name "ngs-sdk")
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(version "1.1.0")
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(source
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(origin
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(method url-fetch)
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(uri
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(string-append "https://github.com/ncbi/ngs/archive/"
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version ".tar.gz"))
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32
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"09fakv9w87lfg9g70kwzmnryqdjj1sz2c7kw01i6drjf787gkjhw"))))
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(build-system gnu-build-system)
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(arguments
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`(#:parallel-build? #f ; not supported
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#:tests? #f ; no "check" target
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#:phases
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(alist-replace
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'configure
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out")))
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;; Only replace the version suffix, not the version number in the
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;; directory name; fixed in commit 46d4509fa8 (no release yet).
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(substitute* "setup/konfigure.perl"
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(((string-append "\\$\\(subst "
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"(\\$\\(VERSION[^\\)]*\\)),"
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"(\\$\\([^\\)]+\\)),"
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"(\\$\\([^\\)]+\\)|\\$\\@)"
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"\\)")
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_ pattern replacement target)
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(string-append "$(patsubst "
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"%" pattern ","
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"%" replacement ","
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target ")")))
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;; The 'configure' script doesn't recognize things like
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;; '--enable-fast-install'.
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(zero? (system* "./configure"
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(string-append "--build-prefix=" (getcwd) "/build")
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(string-append "--prefix=" out)))))
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(alist-cons-after
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'unpack 'enter-dir
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(lambda _ (chdir "ngs-sdk") #t)
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%standard-phases))))
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(native-inputs `(("perl" ,perl)))
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(home-page "https://github.com/ncbi/ngs")
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(synopsis "API for accessing Next Generation Sequencing data")
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(description
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"NGS is a domain-specific API for accessing reads, alignments and pileups
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produced from Next Generation Sequencing. The API itself is independent from
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any particular back-end implementation, and supports use of multiple back-ends
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simultaneously.")
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(license license:public-domain)))
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(define-public seqan
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(package
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(name "seqan")
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