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Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 57 |
1 files changed, 57 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8f1a4ef39f..8c57bd5788 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5356,3 +5356,60 @@ separately. This package provides 15 flavours of betas and three performance metrics, with methods for objects produced by the @code{methylumi} and @code{minfi} packages.") (license license:gpl3))) + +(define-public r-gdsfmt + (package + (name "r-gdsfmt") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gdsfmt" version)) + (sha256 + (base32 + "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy")) + (modules '((guix build utils))) + ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build + ;; them and link with system libraries instead. + (snippet + '(begin + (for-each delete-file-recursively + '("src/LZ4" + "src/XZ" + "src/ZLIB")) + (substitute* "src/Makevars" + (("all: \\$\\(SHLIB\\)") "all:") + (("\\$\\(SHLIB\\): liblzma.a") "") + (("(ZLIB|LZ4)/.*") "") + (("CoreArray/dVLIntGDS.cpp.*") + "CoreArray/dVLIntGDS.cpp") + (("CoreArray/dVLIntGDS.o.*") + "CoreArray/dVLIntGDS.o") + (("PKG_LIBS = ./liblzma.a") + "PKG_LIBS = -llz4")) + (substitute* "src/CoreArray/dStream.h" + (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) + (string-append "include <" header ">"))) + #t)))) + (properties `((upstream-name . "gdsfmt"))) + (build-system r-build-system) + (inputs + `(("lz4" ,lz4) + ("xz" ,xz) + ("zlib" ,zlib))) + (home-page "http://corearray.sourceforge.net/") + (synopsis + "R Interface to CoreArray Genomic Data Structure (GDS) Files") + (description + "This package provides a high-level R interface to CoreArray @dfn{Genomic +Data Structure} (GDS) data files, which are portable across platforms with +hierarchical structure to store multiple scalable array-oriented data sets +with metadata information. It is suited for large-scale datasets, especially +for data which are much larger than the available random-access memory. The +@code{gdsfmt} package offers efficient operations specifically designed for +integers of less than 8 bits, since a diploid genotype, like +@dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a +byte. Data compression and decompression are available with relatively +efficient random access. It is also allowed to read a GDS file in parallel +with multiple R processes supported by the package @code{parallel}.") + (license license:lgpl3))) |