From e1409c764f554b688efe07c04bf90198daeca258 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 25 Jul 2020 00:56:31 +0200 Subject: gnu: check: Update to 0.15.1. * gnu/packages/check.scm (check): Update to 0.15.1. (check-0.14): New public variable. * gnu/packages/backup.scm (burp)[native-inputs]: Change from CHECK to CHECK-0.14. * gnu/packages/bioinformatics.scm (libsbml)[native-inputs]: Likewise. * gnu/packages/databases.scm (recutils)[native-inputs]: Likewise. * gnu/packages/electronics.scm (libsigrokdecode)[native-inputs]: Likewise. * gnu/packages/enlightenment.scm (efl, edi)[native-inputs]: Likewise. * gnu/packages/gnome.scm (gdm)[inputs]: Likewise. * gnu/packages/gtk.scm (girara)[native-inputs]: Likewise. * gnu/packages/messaging.scm (pidgin)[native-inputs]: Likewise. * gnu/packages/networking.scm (iodine)[native-inputs]: Likewise. * gnu/packages/pulseaudio.scm (pulseaudio)[native-inputs]: Likewise. * gnu/packages/sssd.scm (sssd)[native-inputs]: Likewise. * gnu/packages/web.scm (libwapcaplet)[native-inputs]: Likewise. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 681919df3d..4145d9e1f2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15939,7 +15939,7 @@ than is possible with plain-text methods alone.") (propagated-inputs `(("libxml2" ,libxml2))) (native-inputs - `(("check" ,check) + `(("check" ,check-0.14) ("swig" ,swig))) (home-page "http://sbml.org/Software/libSBML") (synopsis "Process SBML files and data streams") -- cgit v1.2.3 From 8c7c6db408ab11e1bed9607d044727af7593151b Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:39 +0200 Subject: gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Move from here... * gnu/packages/bioconductor.scm (r-delayedmatrixstats): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 36 ------------------------------------ 2 files changed, 36 insertions(+), 36 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index db853bfae3..8d7daaeec0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8346,3 +8346,39 @@ routines.") "This package interfaces R with the graphviz library for plotting R graph objects from the @code{graph} package.") (license license:epl1.0))) + +(define-public r-delayedmatrixstats + (package + (name "r-delayedmatrixstats") + (version "1.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DelayedMatrixStats" version)) + (sha256 + (base32 + "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx")))) + (properties + `((upstream-name . "DelayedMatrixStats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-delayedarray" ,r-delayedarray) + ("r-hdf5array" ,r-hdf5array) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") + (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") + (description + "This package provides a port of the @code{matrixStats} API for use with +@code{DelayedMatrix} objects from the @code{DelayedArray} package. It +contains high-performing functions operating on rows and columns of +@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians}, +@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions +are optimized per data type and for subsetted calculations such that both +memory usage and processing time is minimized.") + (license license:expat))) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ffa2618458..ccdc693e08 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10900,42 +10900,6 @@ cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.") (license license:gpl3))) -(define-public r-delayedmatrixstats - (package - (name "r-delayedmatrixstats") - (version "1.10.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DelayedMatrixStats" version)) - (sha256 - (base32 - "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx")))) - (properties - `((upstream-name . "DelayedMatrixStats"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-delayedarray" ,r-delayedarray) - ("r-hdf5array" ,r-hdf5array) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") - (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") - (description - "This package provides a port of the @code{matrixStats} API for use with -@code{DelayedMatrix} objects from the @code{DelayedArray} package. It -contains high-performing functions operating on rows and columns of -@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians}, -@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions -are optimized per data type and for subsetted calculations such that both -memory usage and processing time is minimized.") - (license license:expat))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit v1.2.3 From 1193b77e60a20c2b2751b2abb500d36ab505080e Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:40 +0200 Subject: gnu: r-scran: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-scran): Move from here... * gnu/packages/bioconductor.scm (r-scran): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 ----------------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8d7daaeec0..56ceed36c3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8347,6 +8347,49 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-scran + (package + (name "r-scran") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scran" version)) + (sha256 + (base32 + "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv")))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-bh" ,r-bh) + ("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-dqrng" ,r-dqrng) + ("r-edger" ,r-edger) + ("r-igraph" ,r-igraph) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-s4vectors" ,r-s4vectors) + ("r-scater" ,r-scater) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-statmod" ,r-statmod) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/scran") + (synopsis "Methods for single-cell RNA-Seq data analysis") + (description "This package implements a variety of low-level analyses of +single-cell RNA-seq data. Methods are provided for normalization of +cell-specific biases, assignment of cell cycle phase, and detection of highly +variable and significantly correlated genes.") + (license license:gpl3))) + (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ccdc693e08..dcafbb2d21 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10857,49 +10857,6 @@ 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") - (version "1.16.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "scran" version)) - (sha256 - (base32 - "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv")))) - (build-system r-build-system) - (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-bh" ,r-bh) - ("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-dqrng" ,r-dqrng) - ("r-edger" ,r-edger) - ("r-igraph" ,r-igraph) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scater" ,r-scater) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-statmod" ,r-statmod) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/scran") - (synopsis "Methods for single-cell RNA-Seq data analysis") - (description "This package implements a variety of low-level analyses of -single-cell RNA-seq data. Methods are provided for normalization of -cell-specific biases, assignment of cell cycle phase, and detection of highly -variable and significantly correlated genes.") - (license license:gpl3))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit v1.2.3 From 6b1946b334b9d3808d78dcd7963c0dab2ce7a908 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:41 +0200 Subject: gnu: r-scater: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-scater): Move from here... * gnu/packages/bioconductor.scm (r-scater): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 37 +++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 37 ------------------------------------- 2 files changed, 37 insertions(+), 37 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') 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")) -- cgit v1.2.3 From 916a3e59ab1df1d530f7558b8d653d01a846ee1b Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:42 +0200 Subject: gnu: r-singlecellexperiment: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-singlecellexperiment): Move from here... * gnu/packages/bioconductor.scm (r-singlecellexperiment): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3fec500abb..fbdb7eedb2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8347,6 +8347,35 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-singlecellexperiment + (package + (name "r-singlecellexperiment") + (version "1.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "SingleCellExperiment" version)) + (sha256 + (base32 + "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp")))) + (properties + `((upstream-name . "SingleCellExperiment"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/SingleCellExperiment") + (synopsis "S4 classes for single cell data") + (description "This package defines an S4 class for storing data from +single-cell experiments. This includes specialized methods to store and +retrieve spike-in information, dimensionality reduction coordinates and size +factors for each cell, along with the usual metadata for genes and +libraries.") + (license license:gpl3))) + (define-public r-scater (package (name "r-scater") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8dea6df8a1..ef6d6fc2d8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10791,35 +10791,6 @@ variety of commonly used matrix types, including sparse and HDF5-backed matrices.") (license license:gpl3))) -(define-public r-singlecellexperiment - (package - (name "r-singlecellexperiment") - (version "1.10.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "SingleCellExperiment" version)) - (sha256 - (base32 - "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp")))) - (properties - `((upstream-name . "SingleCellExperiment"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/SingleCellExperiment") - (synopsis "S4 classes for single cell data") - (description "This package defines an S4 class for storing data from -single-cell experiments. This includes specialized methods to store and -retrieve spike-in information, dimensionality reduction coordinates and size -factors for each cell, along with the usual metadata for genes and -libraries.") - (license license:gpl3))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit v1.2.3 From 8863c14cd856d917552017646dbf4a36654e9515 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:43 +0200 Subject: gnu: r-beachmat: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-beachmat): Move from here... * gnu/packages/bioconductor.scm (r-beachmat): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 25 ------------------------- 2 files changed, 25 insertions(+), 25 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fbdb7eedb2..2796f4f90e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8347,6 +8347,31 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-beachmat + (package + (name "r-beachmat") + (version "2.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "beachmat" version)) + (sha256 + (base32 + "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-delayedarray" ,r-delayedarray) + ("r-matrix" ,r-matrix))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/beachmat") + (synopsis "Compiling Bioconductor to handle each matrix type") + (description "This package provides a consistent C++ class interface for a +variety of commonly used matrix types, including sparse and HDF5-backed +matrices.") + (license license:gpl3))) + (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ef6d6fc2d8..a84d19727c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10766,31 +10766,6 @@ block processing.") packages.") (license license:artistic2.0))) -(define-public r-beachmat - (package - (name "r-beachmat") - (version "2.4.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "beachmat" version)) - (sha256 - (base32 - "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/beachmat") - (synopsis "Compiling Bioconductor to handle each matrix type") - (description "This package provides a consistent C++ class interface for a -variety of commonly used matrix types, including sparse and HDF5-backed -matrices.") - (license license:gpl3))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit v1.2.3 From c61268c1b74557bf6b8a26a9c95a47b1bea39d20 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:44 +0200 Subject: gnu: r-rhdf5lib: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-rhdf5lib): Move from here... * gnu/packages/bioconductor.scm (r-rhdf5lib): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 83 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 82 ---------------------------------------- 2 files changed, 83 insertions(+), 82 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2796f4f90e..e7db82741d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2019 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020 Mădălin Ionel Patrașcu +;;; Copyright © 2020 Jakub Kądziołka ;;; ;;; This file is part of GNU Guix. ;;; @@ -8347,6 +8348,88 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-rhdf5lib + (package + (name "r-rhdf5lib") + (version "1.10.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Rhdf5lib" version)) + (sha256 + (base32 + "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete bundled binaries + (delete-file-recursively "src/wininclude/") + (delete-file-recursively "src/winlib-4.9.3/") + (delete-file-recursively "src/winlib-8.3.0/") + (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") + #t)))) + (properties `((upstream-name . "Rhdf5lib"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'do-not-use-bundled-hdf5 + (lambda* (#:key inputs #:allow-other-keys) + (for-each delete-file '("configure" "configure.ac")) + ;; Do not make other packages link with the proprietary libsz. + (substitute* "R/zzz.R" + ((" \"%s/libsz.a\"") "")) + (with-directory-excursion "src" + (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) + (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) + "hdf5") + ;; Remove timestamp and host system information to make + ;; the build reproducible. + (substitute* "hdf5/src/libhdf5.settings.in" + (("Configured on: @CONFIG_DATE@") + "Configured on: Guix") + (("Uname information:.*") + "Uname information: Linux\n") + ;; Remove unnecessary store reference. + (("C Compiler:.*") + "C Compiler: GCC\n")) + (rename-file "Makevars.in" "Makevars") + (substitute* "Makevars" + (("@ZLIB_LIB@") "-lz") + (("@ZLIB_INCLUDE@") "") + (("HDF5_CXX_LIB=.*") + (string-append "HDF5_CXX_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) + (("HDF5_LIB=.*") + (string-append "HDF5_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) + (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") + (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") + (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") + (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") + (("HDF5_HL_LIB=.*") + (string-append "HDF5_HL_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n")) + (("HDF5_HL_CXX_LIB=.*") + (string-append "HDF5_HL_CXX_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) + ;; szip is non-free software + (("cp \"\\$\\{SZIP_LIB\\}.*") "") + (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) + #t))))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("hdf5" ,hdf5-1.10))) + (native-inputs + `(("hdf5-source" ,(package-source hdf5-1.10)) + ("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/Rhdf5lib") + (synopsis "HDF5 library as an R package") + (description "This package provides C and C++ HDF5 libraries for use in R +packages.") + (license license:artistic2.0))) + (define-public r-beachmat (package (name "r-beachmat") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a84d19727c..8bd42c9429 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10684,88 +10684,6 @@ access and manipulation of HDF5 datasets. It supports delayed operations and block processing.") (license license:artistic2.0))) -(define-public r-rhdf5lib - (package - (name "r-rhdf5lib") - (version "1.10.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "Rhdf5lib" version)) - (sha256 - (base32 - "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9")) - (modules '((guix build utils))) - (snippet - '(begin - ;; Delete bundled binaries - (delete-file-recursively "src/wininclude/") - (delete-file-recursively "src/winlib-4.9.3/") - (delete-file-recursively "src/winlib-8.3.0/") - (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz") - #t)))) - (properties `((upstream-name . "Rhdf5lib"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'do-not-use-bundled-hdf5 - (lambda* (#:key inputs #:allow-other-keys) - (for-each delete-file '("configure" "configure.ac")) - ;; Do not make other packages link with the proprietary libsz. - (substitute* "R/zzz.R" - ((" \"%s/libsz.a\"") "")) - (with-directory-excursion "src" - (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) - (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) - "hdf5") - ;; Remove timestamp and host system information to make - ;; the build reproducible. - (substitute* "hdf5/src/libhdf5.settings.in" - (("Configured on: @CONFIG_DATE@") - "Configured on: Guix") - (("Uname information:.*") - "Uname information: Linux\n") - ;; Remove unnecessary store reference. - (("C Compiler:.*") - "C Compiler: GCC\n")) - (rename-file "Makevars.in" "Makevars") - (substitute* "Makevars" - (("@ZLIB_LIB@") "-lz") - (("@ZLIB_INCLUDE@") "") - (("HDF5_CXX_LIB=.*") - (string-append "HDF5_CXX_LIB=" - (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) - (("HDF5_LIB=.*") - (string-append "HDF5_LIB=" - (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) - (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") - (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") - (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") - (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") - (("HDF5_HL_LIB=.*") - (string-append "HDF5_HL_LIB=" - (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n")) - (("HDF5_HL_CXX_LIB=.*") - (string-append "HDF5_HL_CXX_LIB=" - (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) - ;; szip is non-free software - (("cp \"\\$\\{SZIP_LIB\\}.*") "") - (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) - #t))))) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("hdf5" ,hdf5-1.10))) - (native-inputs - `(("hdf5-source" ,(package-source hdf5-1.10)) - ("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/Rhdf5lib") - (synopsis "HDF5 library as an R package") - (description "This package provides C and C++ HDF5 libraries for use in R -packages.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit v1.2.3 From 63b75c01c2374edc38437215278f50b617a12c08 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:47 +0200 Subject: gnu: r-hdf5array: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-hdf5array): Move from here... * gnu/packages/bioconductor.scm (r-hdf5array): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e7db82741d..b2247e8cb6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8348,6 +8348,36 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-hdf5array + (package + (name "r-hdf5array") + (version "1.16.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "HDF5Array" version)) + (sha256 + (base32 + "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn")))) + (properties `((upstream-name . "HDF5Array"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-delayedarray" ,r-delayedarray) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-rhdf5" ,r-rhdf5) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/HDF5Array") + (synopsis "HDF5 back end for DelayedArray objects") + (description "This package provides an array-like container for convenient +access and manipulation of HDF5 datasets. It supports delayed operations and +block processing.") + (license license:artistic2.0))) + (define-public r-rhdf5lib (package (name "r-rhdf5lib") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8bd42c9429..d874fe9a13 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10654,36 +10654,6 @@ quality controls, normalization, visualization, and further analysis are also provided.") (license license:artistic2.0))) -(define-public r-hdf5array - (package - (name "r-hdf5array") - (version "1.16.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "HDF5Array" version)) - (sha256 - (base32 - "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn")))) - (properties `((upstream-name . "HDF5Array"))) - (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rhdf5" ,r-rhdf5) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/HDF5Array") - (synopsis "HDF5 back end for DelayedArray objects") - (description "This package provides an array-like container for convenient -access and manipulation of HDF5 datasets. It supports delayed operations and -block processing.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit v1.2.3 From 7df42d3774778dfbb92e935df720f6eb52965e66 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:45 +0200 Subject: gnu: r-hitc: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-hitc): Move from here... * gnu/packages/bioconductor.scm (r-hitc): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b2247e8cb6..aeb89ae237 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8348,6 +8348,35 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-hitc + (package + (name "r-hitc") + (version "1.32.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "HiTC" version)) + (sha256 + (base32 + "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy")))) + (properties `((upstream-name . "HiTC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rtracklayer" ,r-rtracklayer))) + (home-page "https://bioconductor.org/packages/HiTC") + (synopsis "High throughput chromosome conformation capture analysis") + (description + "The HiTC package was developed to explore high-throughput \"C\" data +such as 5C or Hi-C. Dedicated R classes as well as standard methods for +quality controls, normalization, visualization, and further analysis are also +provided.") + (license license:artistic2.0))) + (define-public r-hdf5array (package (name "r-hdf5array") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d874fe9a13..6bbcc3fe00 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10625,35 +10625,6 @@ intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.") (license license:gpl2+))) -(define-public r-hitc - (package - (name "r-hitc") - (version "1.32.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "HiTC" version)) - (sha256 - (base32 - "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy")))) - (properties `((upstream-name . "HiTC"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer))) - (home-page "https://bioconductor.org/packages/HiTC") - (synopsis "High throughput chromosome conformation capture analysis") - (description - "The HiTC package was developed to explore high-throughput \"C\" data -such as 5C or Hi-C. Dedicated R classes as well as standard methods for -quality controls, normalization, visualization, and further analysis are also -provided.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit v1.2.3 From 3292f6eda0a89f65a0e3d5c0dc9fee71895dfa25 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 14 Sep 2020 18:07:46 +0200 Subject: gnu: r-fithic: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-fithic): Move from here... * gnu/packages/bioconductor.scm (r-fithic): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 26 -------------------------- 2 files changed, 26 insertions(+), 26 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aeb89ae237..f52025da91 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8348,6 +8348,32 @@ routines.") objects from the @code{graph} package.") (license license:epl1.0))) +(define-public r-fithic + (package + (name "r-fithic") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "FitHiC" version)) + (sha256 + (base32 + "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp")))) + (properties `((upstream-name . "FitHiC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-fdrtool" ,r-fdrtool) + ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/FitHiC") + (synopsis "Confidence estimation for intra-chromosomal contact maps") + (description + "Fit-Hi-C is a tool for assigning statistical confidence estimates to +intra-chromosomal contact maps produced by genome-wide genome architecture +assays such as Hi-C.") + (license license:gpl2+))) + (define-public r-hitc (package (name "r-hitc") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6bbcc3fe00..71369affaf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10599,32 +10599,6 @@ EMBL-EBI GWAS catalog.") visualizations for publication-quality multi-panel figures.") (license license:gpl2+))) -(define-public r-fithic - (package - (name "r-fithic") - (version "1.14.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "FitHiC" version)) - (sha256 - (base32 - "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp")))) - (properties `((upstream-name . "FitHiC"))) - (build-system r-build-system) - (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-fdrtool" ,r-fdrtool) - ("r-rcpp" ,r-rcpp))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/FitHiC") - (synopsis "Confidence estimation for intra-chromosomal contact maps") - (description - "Fit-Hi-C is a tool for assigning statistical confidence estimates to -intra-chromosomal contact maps produced by genome-wide genome architecture -assays such as Hi-C.") - (license license:gpl2+))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit v1.2.3 From d27ec8db70ac2fb41789140a7955d4fa26c61666 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 22 Sep 2020 11:12:52 +0200 Subject: gnu: mafft: Use HTTPS home page URI. * gnu/packages/bioinformatics.scm (mafft)[home-page, license]: Use HTTPS URI. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 71369affaf..4376897d37 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4568,7 +4568,7 @@ sequencing tag position and orientation.") ("gawk" ,gawk) ("grep" ,grep) ("coreutils" ,coreutils))) - (home-page "http://mafft.cbrc.jp/alignment/software/") + (home-page "https://mafft.cbrc.jp/alignment/software/") (synopsis "Multiple sequence alignment program") (description "MAFFT offers a range of multiple alignment methods for nucleotide and @@ -4576,7 +4576,7 @@ protein sequences. For instance, it offers L-INS-i (accurate; for alignment of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000 sequences).") (license (license:non-copyleft - "http://mafft.cbrc.jp/alignment/software/license.txt" + "https://mafft.cbrc.jp/alignment/software/license.txt" "BSD-3 with different formatting")))) (define-public mash -- cgit v1.2.3 From 0990d6119336cb6142020dc577f57f1faffe55ba Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 24 Sep 2020 23:11:19 +0200 Subject: gnu: mafft: Update to 7.471. * gnu/packages/bioinformatics.scm (mafft): Update to 7.471. Signed-off-by: Mathieu Othacehe --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4376897d37..fda7255662 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2017 Arun Isaac ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits -;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu +;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu ;;; Copyright © 2019 Maxim Cournoyer ;;; Copyright © 2019 Brian Leung ;;; Copyright © 2019 Brett Gilio @@ -4496,7 +4496,7 @@ sequencing tag position and orientation.") (define-public mafft (package (name "mafft") - (version "7.394") + (version "7.471") (source (origin (method url-fetch) (uri (string-append @@ -4505,7 +4505,7 @@ sequencing tag position and orientation.") (file-name (string-append name "-" version ".tgz")) (sha256 (base32 - "0bacjkxfg944p5khhyh5rd4y7wkjc9qk4v2jjj442sqlq0f8ar7b")))) + "0r1973fx2scq4712zdqfy67wkzqj0c0bhrdy4jxhvq40mdxyry30")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no automated tests, though there are tests in the read me -- cgit v1.2.3 From 78d9fbd2fd88b1811c52228abe978a5a743bc347 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Oct 2020 13:12:05 +0200 Subject: gnu: r-biocstyle: Update to 2.16.1. * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fda7255662..5ec3f617af 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7539,13 +7539,13 @@ also known as views, in a controlled vocabulary.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.16.0") + (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "07rjl2n4sazdg581zh7w3yykzphgr2gpz41ba4ryqs7347vh9nbf")))) + "09sz2bnbfbj8wz16k0q8xrvag9fldxqyp5vbg9pvd9skh28hv7c7")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) -- cgit v1.2.3 From 906c79d1a3c94ffa544473651e9e8cef60b122cd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Oct 2020 13:12:08 +0200 Subject: gnu: r-rhdf5: Update to 2.32.3. * gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5ec3f617af..846a5f2e22 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8848,13 +8848,13 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.32.2") + (version "2.32.3") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "1v6ygi0avh3gmaj2ld2nr7vww4ipw39b5kqci9w27i3ja985lb8j")))) + "0fnx60dpf6s2qwq48lg98g18g8k7wgm66pw0kamlbb7l2hnwycvf")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5lib" ,r-rhdf5lib))) -- cgit v1.2.3 From 73a2fe4ab75754418b90c73494adf5542e8f172f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Oct 2020 13:12:11 +0200 Subject: gnu: r-gqtlbase: Update to 1.20.4. * gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 846a5f2e22..3957ae299b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10272,14 +10272,14 @@ interval to data view, mismatch pileup, and several splicing summaries.") (define-public r-gqtlbase (package (name "r-gqtlbase") - (version "1.20.0") + (version "1.20.4") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLBase" version)) (sha256 (base32 - "06xvzp4fn3qfa46ggg8kxi267gbyd821vvx4040173xkqxpr0g5j")))) + "1ly14vhhqxjpbxjypi6ppd37dycabdhf4ny4nsvp9969k418zv41")))) (properties `((upstream-name . "gQTLBase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From fb0037af8cecc0ebaa330392b0c54a35b7b8a424 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 7 Oct 2020 15:33:28 +0200 Subject: gnu: htslib: Enable support for custom URI schemes. * gnu/packages/bioinformatics.scm (htslib)[arguments]: Enable support for custom URIs. --- gnu/packages/bioinformatics.scm | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3957ae299b..fefca80e9e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4225,6 +4225,13 @@ performance.") (base32 "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0")))) (build-system gnu-build-system) + ;; Let htslib translate "gs://" and "s3://" to regular https links with + ;; "--enable-gcs" and "--enable-s3". For these options to work, we also + ;; need to set "--enable-libcurl". + (arguments + `(#:configure-flags '("--enable-gcs" + "--enable-libcurl" + "--enable-s3"))) (inputs `(("curl" ,curl) ("openssl" ,openssl))) -- cgit v1.2.3 From 997abda92b75a1173130f45ea840c390db2b1a23 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Oct 2020 17:23:11 +0200 Subject: gnu: Remove redundant MariaDB inputs. For well-behaved build systems, including the "dev" output suffices. * gnu/packages/bioinformatics.scm (kentutils)[inputs]: Remove MARIADB:LIB. * gnu/packages/cran.scm (r-rmysql)[inputs]: Likewise. * gnu/packages/databases.scm (python-mysqlclient, soci)[inputs]: Likewise. * gnu/packages/qt.scm (qt-4, qtbase): Likewise. * gnu/packages/ruby.scm (ruby-mysql2)[inputs]: Likewise. --- gnu/packages/bioinformatics.scm | 1 - gnu/packages/cran.scm | 3 +-- gnu/packages/databases.scm | 6 ++---- gnu/packages/kodi.scm | 2 +- gnu/packages/qt.scm | 2 -- gnu/packages/ruby.scm | 3 +-- 6 files changed, 5 insertions(+), 12 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b0edfa8403..0d5e6e3d20 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11154,7 +11154,6 @@ models. TADbit is complemented by TADkit for visualizing 3D models.") ("tcsh" ,tcsh) ("perl" ,perl) ("libpng" ,libpng) - ("mariadb" ,mariadb "lib") ("mariadb-dev" ,mariadb "dev") ("openssl" ,openssl-1.0))) (home-page "https://genome.cse.ucsc.edu/index.html") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 59a409f8e9..463e9d4279 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3327,8 +3327,7 @@ dimensioned arrays.") (properties `((upstream-name . "RMySQL"))) (build-system r-build-system) (inputs - `(("mariadb" ,mariadb "lib") - ("mariadb-dev" ,mariadb "dev") + `(("mariadb-dev" ,mariadb "dev") ("zlib" ,zlib))) (propagated-inputs `(("r-dbi" ,r-dbi))) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 7bce37c3e9..2d4b5cf129 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -2990,8 +2990,7 @@ database).") (build-system python-build-system) (arguments '(#:tests? #f)) ;XXX: requires a live database (inputs - `(("mysql" ,mariadb "lib") - ("mysql-dev" ,mariadb "dev"))) + `(("mysql-dev" ,mariadb "dev"))) (home-page "https://github.com/PyMySQL/mysqlclient-python") (synopsis "MySQLdb is an interface to the popular MySQL database server for Python") (description "MySQLdb is an interface to the popular MySQL database server @@ -3672,8 +3671,7 @@ The drivers officially supported by @code{libdbi} are: ("sqlite" ,sqlite) ("odbc" ,unixodbc) ("boost" ,boost) - ("mariadb:dev" ,mariadb "dev") - ("mariadb:lib" ,mariadb "lib"))) + ("mariadb:dev" ,mariadb "dev"))) (arguments `(#:tests? #f ; Tests may require running database management systems. #:phases diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm index 2edf5c0614..9ccdea46ef 100644 --- a/gnu/packages/kodi.scm +++ b/gnu/packages/kodi.scm @@ -435,7 +435,7 @@ alternatives. In compilers, this can reduce the cascade of secondary errors.") ("libxrender" ,libxrender) ("libxslt" ,libxslt) ("lzo" ,lzo) - ("mariadb" ,mariadb "lib") + ("mariadb-dev" ,mariadb "lib") ("mariadb-dev" ,mariadb "dev") ("openssl" ,openssl) ("pcre" ,pcre) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index a596ca4ce6..aabbdc308f 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -195,7 +195,6 @@ system, and the core design of Django is reused in Grantlee.") ("libxslt" ,libxslt) ("libxtst" ,libxtst) ("mtdev" ,mtdev) - ("mariadb" ,mariadb "lib") ("mariadb-dev" ,mariadb "dev") ("nss" ,nss) ("postgresql" ,postgresql) @@ -406,7 +405,6 @@ developers using C++ or QML, a CSS & JavaScript like language.") ("libxslt" ,libxslt) ("libxtst" ,libxtst) ("mtdev" ,mtdev) - ("mariadb" ,mariadb "lib") ("mariadb-dev" ,mariadb "dev") ("nss" ,nss) ("openssl" ,openssl) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 7348f29eb1..cd452f88d3 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -3795,8 +3795,7 @@ specs for Ruby implementations in ruby/spec.") (invoke "rspec")) #t))))) (inputs - `(("mariadb" ,mariadb "lib") - ("mariadb-dev" ,mariadb "dev") + `(("mariadb-dev" ,mariadb "dev") ("zlib" ,zlib))) (native-inputs `(("ruby-rspec" ,ruby-rspec) -- cgit v1.2.3