gnu: Add smithlab-cpp.

* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
This commit is contained in:
Ricardo Wurmus 2015-11-20 11:14:00 +01:00
parent 3d51ec919e
commit c6a24d6e92
1 changed files with 53 additions and 0 deletions

View File

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