gnu: Add r-gdsfmt.
* gnu/packages/bioconductor.scm (r-gdsfmt): New variable.
This commit is contained in:
parent
38babeaaa4
commit
7d2cb646f7
|
@ -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)))
|
||||
|
|
Loading…
Reference in New Issue