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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-11-20 11:14:00 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-11-20 15:22:06 +0100
commitc6a24d6e92c730d03dcfcde231fd6e7dece908ca (patch)
treeed1f188a48783a9afa0203b184700d59aa36a7df /gnu
parent3d51ec919ed5e6a6a650b6f1007e2688bc942329 (diff)
downloadpatches-c6a24d6e92c730d03dcfcde231fd6e7dece908ca.tar
patches-c6a24d6e92c730d03dcfcde231fd6e7dece908ca.tar.gz
gnu: Add smithlab-cpp.
* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm53
1 files changed, 53 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ace30bdbd1..4ae1ad0470 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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")