diff options
author | Ricardo Wurmus <rekado@elephly.net> | 2018-02-12 15:18:49 +0100 |
---|---|---|
committer | Ricardo Wurmus <rekado@elephly.net> | 2018-02-12 15:29:43 +0100 |
commit | 748e9f163a06b6812dfdccb2ccefcebb5cd60dcb (patch) | |
tree | ddb973f4ac579212356d7606b562b2d66879c685 /gnu | |
parent | d2c0f03037085ad7cd22dcaf6dadab9b914be52a (diff) | |
download | patches-748e9f163a06b6812dfdccb2ccefcebb5cd60dcb.tar patches-748e9f163a06b6812dfdccb2ccefcebb5cd60dcb.tar.gz |
gnu: Add r-rhdf5lib.
* gnu/packages/bioinformatics.scm (r-rhdf5lib): New variable.
Diffstat (limited to 'gnu')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 56 |
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 |