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context:2020-01-15import: cpan: Rewrite tests to use an HTTP server instead of mocking....* guix/import/cpan.scm (%metacpan-base-url): New variable. (module->dist-name, cpan-fetch): Refer to it instead of the hard-coded URL. * tests/cpan.scm ("cpan->guix-package"): Use 'with-http-server' instead of 'mock'. Ludovic Courtès
2020-01-15import: cpan: Rewrite to use 'define-json-mapping'....* guix/import/cpan.scm (<cpan-dependency>, <cpan-release>): New JSON-mapped record types. (metacpan-url->mirror-url): New procedure. (cpan-source-url): Rewrite in terms of it. (cpan-version): Remove. (cpan-module->sexp): Rewrite to take a <cpan-release> instead of an alist, and rename 'meta' to 'release'. [convert-inputs]: Rewrite to use 'cpan-release-dependencies'. Update calls to 'convert-inputs' to pass a list of symbols. Replace 'assoc-ref' calls with the appropriate field accessors. (cpan->guix-package): Rename 'module-meta' to 'release'. (latest-release): Likewise, and use the appropriate accessors. * tests/cpan.scm (test-json): Remove "prereqs" record; add "dependency" list. ("source-url-http", "source-url-https"): Remove. ("metacpan-url->mirror-url, http") ("metacpan-url->mirror-url, https"): New tests. Ludovic Courtès
2 files changed, 37 insertions, 37 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 56ceed36c3..3fec500abb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8347,6 +8347,43 @@ routines.")
objects from the @code{graph} package.")
(license license:epl1.0)))
+(define-public r-scater
+ (package
+ (name "r-scater")
+ (version "1.16.2")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "scater" version))
+ (sha256
+ (base32
+ "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-beachmat" ,r-beachmat)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocneighbors" ,r-biocneighbors)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biocsingular" ,r-biocsingular)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+ ("r-ggbeeswarm" ,r-ggbeeswarm)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rlang" ,r-rlang)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-viridis" ,r-viridis)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/davismcc/scater")
+ (synopsis "Single-cell analysis toolkit for gene expression data in R")
+ (description "This package provides a collection of tools for doing
+various analyses of single-cell RNA-seq gene expression data, with a focus on
+quality control.")
+ (license license:gpl2+)))
+
(define-public r-scran
(package
(name "r-scran")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dcafbb2d21..8dea6df8a1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10820,43 +10820,6 @@ factors for each cell, along with the usual metadata for genes and
libraries.")
(license license:gpl3)))
-(define-public r-scater
- (package
- (name "r-scater")
- (version "1.16.2")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "scater" version))
- (sha256
- (base32
- "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-beachmat" ,r-beachmat)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocneighbors" ,r-biocneighbors)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biocsingular" ,r-biocsingular)
- ("r-delayedarray" ,r-delayedarray)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-ggbeeswarm" ,r-ggbeeswarm)
- ("r-ggplot2" ,r-ggplot2)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-rlang" ,r-rlang)
- ("r-s4vectors" ,r-s4vectors)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-viridis" ,r-viridis)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/davismcc/scater")
- (synopsis "Single-cell analysis toolkit for gene expression data in R")
- (description "This package provides a collection of tools for doing
-various analyses of single-cell RNA-seq gene expression data, with a focus on
-quality control.")
- (license license:gpl2+)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
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