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authorRicardo Wurmus <rekado@elephly.net>2018-02-12 15:18:49 +0100
committerRicardo Wurmus <rekado@elephly.net>2018-02-12 15:29:43 +0100
commit748e9f163a06b6812dfdccb2ccefcebb5cd60dcb (patch)
treeddb973f4ac579212356d7606b562b2d66879c685 /gnu/packages/bioinformatics.scm
parentd2c0f03037085ad7cd22dcaf6dadab9b914be52a (diff)
downloadpatches-748e9f163a06b6812dfdccb2ccefcebb5cd60dcb.tar
patches-748e9f163a06b6812dfdccb2ccefcebb5cd60dcb.tar.gz
gnu: Add r-rhdf5lib.
* gnu/packages/bioinformatics.scm (r-rhdf5lib): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm56
1 files changed, 56 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9c8ff7be0c..0dbb1f1764 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10428,6 +10428,62 @@ access and manipulation of HDF5 datasets. It supports delayed operations and
block processing.")
(license license:artistic2.0)))
+(define-public r-rhdf5lib
+ (package
+ (name "r-rhdf5lib")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rhdf5lib" version))
+ (sha256
+ (base32
+ "0kkc4rprjbqn2wvbx4d49kk9l91vihccxbl4843qr1wqk6v33r1w"))))
+ (properties `((upstream-name . "Rhdf5lib")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'do-not-use-bundled-hdf5
+ (lambda* (#:key inputs #:allow-other-keys)
+ (for-each delete-file '("configure" "configure.ac"))
+ ;; Do not make other packages link with the proprietary libsz.
+ (substitute* "R/zzz.R"
+ (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a'")
+ "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a'")
+ (("'%s/libhdf5.a %s/libsz.a'")
+ "'%s/libhdf5.a %s/libhdf5.a'"))
+ (with-directory-excursion "src"
+ (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
+ (rename-file (string-append "hdf5-" ,(package-version hdf5))
+ "hdf5")
+ (rename-file "Makevars.in" "Makevars")
+ (substitute* "Makevars"
+ (("HDF5_CXX_LIB=.*")
+ (string-append "HDF5_CXX_LIB="
+ (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
+ (("HDF5_LIB=.*")
+ (string-append "HDF5_LIB="
+ (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
+ (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
+ (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
+ ;; szip is non-free software
+ (("cp \\$\\{SZIP_LIB\\}.*") "")
+ (("PKG_LIBS = \\$\\{HDF5_LIB\\} \\$\\{SZIP_LIB\\}")
+ "PKG_LIBS = ${HDF5_LIB}\n")))
+ #t)))))
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("hdf5" ,hdf5)))
+ (native-inputs
+ `(("hdf5-source" ,(package-source hdf5))))
+ (home-page "https://bioconductor.org/packages/Rhdf5lib")
+ (synopsis "HDF5 library as an R package")
+ (description "This package provides C and C++ HDF5 libraries for use in R
+packages.")
+ (license license:artistic2.0)))
+
(define htslib-for-sambamba
(let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
(package