Mădălin Ionel Patrașcu wrote 4 years ago
(address . guix-patches@gnu.org)
10231918-e505-c813-7573-b7e8f9fb4eee@mdc-berlin.de
(no subject)
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- 2 participants
- Mădălin Ionel Patrașcu
- Ricardo Wurmus
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- Mădălin Ionel Patrașcu
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Mădălin Ionel Patrașcu wrote 4 years ago
[PATCH 1/3] gnu: Add r-rcppthread.
(address . 46937@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)
20210305012039.15219-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/cran.scm (r-rcppthread): New variable.
---
gnu/packages/cran.scm | 23 ++++++++++++++++++++++-
1 file changed, 22 insertions(+), 1 deletion(-)
Toggle diff (43 lines)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1d574b9768..4ac4b4cae1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11,7 +11,7 @@
;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
-;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2018, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
@@ -2668,6 +2668,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
@code{citation(\"Rcpp\")} for details on these last two.")
(license license:gpl2+)))
+(define-public r-rcppthread
+ (package
+ (name "r-rcppthread")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "RcppThread" version))
+ (sha256
+ (base32
+ "1xfcxrny779kgknlvnc4j02ifprnakndnkhx8bhy50d39vp4hjjl"))))
+ (properties `((upstream-name . "RcppThread")))
+ (build-system r-build-system)
+ (home-page
+ "https://github.com/tnagler/RcppThread")
+ (synopsis "R threading in C++")
+ (description
+ "This package provides a C++11-style thread class and thread pool that can
+safely be interrupted from R.")
+ (license license:expat)))
+
(define-public r-bindr
(package
(name "r-bindr")
--
2.30.1
Mădălin Ionel Patrașcu wrote 4 years ago
[PATCH 2/3] gnu: Add r-universalmotif.
(address . 46937@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)
20210305012039.15219-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-universalmotif): New variable.
---
gnu/packages/bioconductor.scm | 53 ++++++++++++++++++++++++++++++++++-
1 file changed, 52 insertions(+), 1 deletion(-)
Toggle diff (73 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a4d97fad65..55a9b07509 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4,7 +4,7 @@
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019, 2020 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
-;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;;
;;; This file is part of GNU Guix.
@@ -7435,6 +7435,57 @@ data. This modified test allows for testing differential expression in qPCR
data.")
(license license:gpl2+)))
+(define-public r-universalmotif
+ (package
+ (name "r-universalmotif")
+ (version "1.8.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "universalmotif" version))
+ (sha256
+ (base32
+ "1ys2kbayc1rzv8nzi60208yfslm4kzynndfg7vw2n0c30dvzycrc"))))
+ (properties
+ `((upstream-name . "universalmotif")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-link
+ (lambda _
+ (substitute* "src/Makevars"
+ (("/usr/bin/strip") (which "strip")))
+ #t)))))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggseqlogo" ,r-ggseqlogo)
+ ("r-iranges" ,r-iranges)
+ ("r-mass" ,r-mass)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppthread" ,r-rcppthread)
+ ("r-rdpack" ,r-rdpack)
+ ("r-rlang" ,r-rlang)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-yaml" ,r-yaml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page
+ "https://bioconductor.org/packages/universalmotif/")
+ (synopsis
+ "Specific structures importer, modifier, and exporter for R")
+ (description
+ "This package allows importing most common @dfn{specific structure}
+(motif) types into R for use by functions provided by other Bioconductor
+motif-related packages. Motifs can be exported into most major motif formats
+from various classes as defined by other Bioconductor packages. A suite of
+motif and sequence manipulation and analysis functions are included, including
+enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
+motifs, and others.")
+ (license license:gpl3)))
+
;; This is a CRAN package, but it depends on Bioconductor packages, so we put
;; it here.
(define-public r-activedriverwgs
--
2.30.1
Mădălin Ionel Patrașcu wrote 4 years ago
[PATCH 3/3] gnu: Add r-circrnaprofiler.
(address . 46937@debbugs.gnu.org)(address . rekado@elephly.net)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)
20210305012039.15219-3-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-circrnaprofiler): New variable.
---
gnu/packages/bioconductor.scm | 53 +++++++++++++++++++++++++++++++++++
1 file changed, 53 insertions(+)
Toggle diff (66 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 55a9b07509..2da2be6ae3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6810,6 +6810,59 @@ accessibility data.")
,@(alist-delete "r-monocle"
(package-propagated-inputs r-cicero)))))))
+(define-public r-circrnaprofiler
+ (package
+ (name "r-circrnaprofiler")
+ (version "1.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "circRNAprofiler" version))
+ (sha256
+ (base32
+ "1rwpl9a5p5242aiapik0vf4ywqh7m6phzl8z8qmzcy0imbx7mpbn"))))
+ (properties
+ `((upstream-name . "circRNAprofiler")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationhub" ,r-annotationhub)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+ ("r-deseq2" ,r-deseq2)
+ ("r-dplyr" ,r-dplyr)
+ ("r-edger" ,r-edger)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gwascat" ,r-gwascat)
+ ("r-iranges" ,r-iranges)
+ ("r-magrittr" ,r-magrittr)
+ ("r-r-utils" ,r-r-utils)
+ ("r-readr" ,r-readr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rlang" ,r-rlang)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-seqinr" ,r-seqinr)
+ ("r-stringi" ,r-stringi)
+ ("r-stringr" ,r-stringr)
+ ("r-universalmotif" ,r-universalmotif)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page
+ "https://github.com/Aufiero/circRNAprofiler")
+ (synopsis
+ "Computational framework for the downstream analysis of circular RNA's")
+ (description
+ "@code{r-circrnaprofiler} is a computational framework for a comprehensive
+in silico analysis of @dfn{circular RNA} (circRNAs). This computational
+framework allows to combine and analyze circRNAs previously detected by
+multiple publicly available annotation-based circRNA detection tools. It
+covers different aspects of circRNAs analysis from differential expression
+analysis, evolutionary conservation, biogenesis to functional analysis.")
+ (license license:gpl3)))
+
(define-public r-cistopic
(let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
(revision "0"))
--
2.30.1
Ricardo Wurmus wrote 4 years ago
Re: [PATCH 1/3] gnu: Add r-rcppthread.
(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 46937-done@debbugs.gnu.org)
87ft19tyme.fsf@elephly.net
Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:
Toggle quote (4 lines)
> * gnu/packages/cran.scm (r-rcppthread): New variable. […]
> * gnu/packages/bioconductor.scm (r-universalmotif): New variable. […]
> * gnu/packages/bioconductor.scm (r-circrnaprofiler): New variable.
Applied with minor changes: we no longer end phases with #t.
Thank you!
--
Ricardo
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