gnu: Add smithlab-cpp.
* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
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@ -2534,6 +2534,59 @@ subsequent visualization, annotation and storage of results.")
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;; LGPLv2.1+
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(license (list license:gpl2 license:lgpl2.1+))))
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(define-public smithlab-cpp
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(let ((revision "1")
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(commit "728a097"))
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(package
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(name "smithlab-cpp")
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(version (string-append "0." revision "." commit))
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/smithlabcode/smithlab_cpp.git")
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(commit commit)))
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(file-name (string-append name "-" version "-checkout"))
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(sha256
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(base32
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"0d476lmj312xk77kr9fzrv7z1bv96yfyx0w7y62ycmnfbx32ll74"))))
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(build-system gnu-build-system)
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(arguments
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`(#:modules ((guix build gnu-build-system)
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(guix build utils)
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(srfi srfi-26))
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#:tests? #f ;no "check" target
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'use-samtools-headers
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(lambda _
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(substitute* '("SAM.cpp"
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"SAM.hpp")
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(("sam.h") "samtools/sam.h"))
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#t))
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(lib (string-append out "/lib"))
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(include (string-append out "/include/smithlab-cpp")))
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(mkdir-p lib)
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(mkdir-p include)
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(for-each (cut install-file <> lib)
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(find-files "." "\\.o$"))
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(for-each (cut install-file <> include)
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(find-files "." "\\.hpp$")))
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#t))
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(delete 'configure))))
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(inputs
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`(("samtools" ,samtools-0.1)
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("zlib" ,zlib)))
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(home-page "https://github.com/smithlabcode/smithlab_cpp")
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(synopsis "C++ helper library for functions used in Smith lab projects")
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(description
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"Smithlab CPP is a C++ library that includes functions used in many of
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the Smith lab bioinformatics projects, such as a wrapper around Samtools data
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structures, classes for genomic regions, mapped sequencing reads, etc.")
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(license license:gpl3+))))
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(define-public preseq
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(package
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(name "preseq")
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