mirror of
https://git.savannah.gnu.org/git/guix.git
synced 2025-01-19 05:57:04 +01:00
gnu: r-mzr: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-mzr): Move from here... * gnu/packages/bioconductor.scm (r-mzr): ...to here.
This commit is contained in:
zimoun
Ricardo Wurmus
parent
88cf24febb
commit
720d2694a5
2 changed files with 62 additions and 61 deletions
|
|
@ -36,6 +36,7 @@ (define-module (gnu packages bioconductor)
|
|||
#:use-module (gnu packages)
|
||||
#:use-module (gnu packages base)
|
||||
#:use-module (gnu packages bioinformatics)
|
||||
#:use-module (gnu packages boost)
|
||||
#:use-module (gnu packages cran)
|
||||
#:use-module (gnu packages compression)
|
||||
#:use-module (gnu packages gcc)
|
||||
|
|
@ -3256,6 +3257,67 @@ (define-public r-mzid
|
|||
specific parser.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public r-mzr
|
||||
(package
|
||||
(name "r-mzr")
|
||||
(version "2.24.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "mzR" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(begin
|
||||
(delete-file-recursively "src/boost")
|
||||
#t))))
|
||||
(properties `((upstream-name . "mzR")))
|
||||
(build-system r-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'use-system-boost
|
||||
(lambda _
|
||||
(substitute* "src/Makevars"
|
||||
(("\\./boost/libs.*") "")
|
||||
;; This is to avoid having a plain directory on the list of
|
||||
;; libraries to link.
|
||||
(("\\(RHDF5_LIBS\\)" match)
|
||||
(string-append match "/libhdf5.a"))
|
||||
(("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
|
||||
(("\\ARCH_OBJS=" line)
|
||||
(string-append line
|
||||
"\nBOOST_LIBS=-lboost_system -lboost_regex \
|
||||
-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
|
||||
#t)))))
|
||||
(inputs
|
||||
`(;; Our default boost package won't work here, unfortunately, even with
|
||||
;; mzR version 2.24.1.
|
||||
("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
|
||||
("zlib" ,zlib)))
|
||||
(propagated-inputs
|
||||
`(("r-biobase" ,r-biobase)
|
||||
("r-biocgenerics" ,r-biocgenerics)
|
||||
("r-ncdf4" ,r-ncdf4)
|
||||
("r-protgenerics" ,r-protgenerics)
|
||||
("r-rcpp" ,r-rcpp)
|
||||
("r-rhdf5lib" ,r-rhdf5lib)
|
||||
("r-zlibbioc" ,r-zlibbioc)))
|
||||
(native-inputs
|
||||
`(("r-knitr" ,r-knitr)))
|
||||
(home-page "https://github.com/sneumann/mzR/")
|
||||
(synopsis "Parser for mass spectrometry data files")
|
||||
(description
|
||||
"The mzR package provides a unified API to the common file formats and
|
||||
parsers available for mass spectrometry data. It comes with a wrapper for the
|
||||
ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
|
||||
The package contains the original code written by the ISB, and a subset of the
|
||||
proteowizard library for mzML and mzIdentML. The netCDF reading code has
|
||||
previously been used in XCMS.")
|
||||
(license license:artistic2.0)))
|
||||
|
||||
(define-public r-organismdbi
|
||||
(package
|
||||
(name "r-organismdbi")
|
||||
|
|
|
|||
|
|
@ -9047,67 +9047,6 @@ (define-public r-protgenerics
|
|||
proteomics packages.")
|
||||
(license license:artistic2.0)))
|
||||
|
||||
(define-public r-mzr
|
||||
(package
|
||||
(name "r-mzr")
|
||||
(version "2.24.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (bioconductor-uri "mzR" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg"))
|
||||
(modules '((guix build utils)))
|
||||
(snippet
|
||||
'(begin
|
||||
(delete-file-recursively "src/boost")
|
||||
#t))))
|
||||
(properties `((upstream-name . "mzR")))
|
||||
(build-system r-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'use-system-boost
|
||||
(lambda _
|
||||
(substitute* "src/Makevars"
|
||||
(("\\./boost/libs.*") "")
|
||||
;; This is to avoid having a plain directory on the list of
|
||||
;; libraries to link.
|
||||
(("\\(RHDF5_LIBS\\)" match)
|
||||
(string-append match "/libhdf5.a"))
|
||||
(("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
|
||||
(("\\ARCH_OBJS=" line)
|
||||
(string-append line
|
||||
"\nBOOST_LIBS=-lboost_system -lboost_regex \
|
||||
-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
|
||||
#t)))))
|
||||
(inputs
|
||||
`(;; Our default boost package won't work here, unfortunately, even with
|
||||
;; mzR version 2.24.1.
|
||||
("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
|
||||
("zlib" ,zlib)))
|
||||
(propagated-inputs
|
||||
`(("r-biobase" ,r-biobase)
|
||||
("r-biocgenerics" ,r-biocgenerics)
|
||||
("r-ncdf4" ,r-ncdf4)
|
||||
("r-protgenerics" ,r-protgenerics)
|
||||
("r-rcpp" ,r-rcpp)
|
||||
("r-rhdf5lib" ,r-rhdf5lib)
|
||||
("r-zlibbioc" ,r-zlibbioc)))
|
||||
(native-inputs
|
||||
`(("r-knitr" ,r-knitr)))
|
||||
(home-page "https://github.com/sneumann/mzR/")
|
||||
(synopsis "Parser for mass spectrometry data files")
|
||||
(description
|
||||
"The mzR package provides a unified API to the common file formats and
|
||||
parsers available for mass spectrometry data. It comes with a wrapper for the
|
||||
ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
|
||||
The package contains the original code written by the ISB, and a subset of the
|
||||
proteowizard library for mzML and mzIdentML. The netCDF reading code has
|
||||
previously been used in XCMS.")
|
||||
(license license:artistic2.0)))
|
||||
|
||||
(define-public r-dropbead
|
||||
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
|
||||
(revision "2"))
|
||||
|
|
|
|||
Loading…
Reference in a new issue