From: Ra <ilpuccio.febo@gmail.com>
To: guix-devel <guix-devel@gnu.org>
Subject: [PATCH] Add r-scran 1.2.0 and all its dependencies
Date: Tue, 27 Dec 2016 09:14:30 +0000 [thread overview]
Message-ID: <CACQsWTNkoAAg=u8riwECrb=Ae9cRyHuOE_HUcX=L5NBV4nE2Aw@mail.gmail.com> (raw)
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Hi devs,
in attachment a patch for the inclusion of an R/Bioconductor library named
"scran" https://bioconductor.org/packages/release/bioc/html/scran.html ,
scran has a lot of dependencies and I placed those related to
bioinformatics/bioconductor into bioinformatics.scm and those related just
to R insto statistics.scm.
There are a total of 11 new R libraries in this patch and the most
complicated is the r-rhdf5 where I had to modify a bit the original
installation because it contains a sub_tar_archive ( I had a brief
discussion with Rekado on irc - I saw your message/replay today- ).
Let me know if this big-patch is acceptable or how do I need to submit it.
Thanks a lot.
Raoul
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From b64c564c0d7719732e672116269690c4d00d3422 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Tue, 27 Dec 2016 09:32:42 +0100
Subject: [PATCH] Add r-scran 1.2.0 and all its dependencies
---
gnu/packages/bioinformatics.scm | 132 ++++++++++++++++++++++++++++++++++
gnu/packages/statistics.scm | 156 ++++++++++++++++++++++++++++++++++++++++
2 files changed, 288 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 912941e..d20da9a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7876,3 +7876,135 @@ replacement for strverscmp.")
samples into a single report. It contains modules for a large number of
common bioinformatics tools.")
(license license:gpl3)))
+
+(define-public r-scran
+(package
+ (name "r-scran")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "scran" version))
+ (sha256
+ (base32
+ "1wnsmp46x9zgbiacf9hxhpy42gxbvwf8q2x6dchc3r9g4p2s65c5"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-dynamictreecut" ,r-dynamictreecut)
+ ("r-edger" ,r-edger)
+ ("r-scater" ,r-scater)
+ ("r-shiny" ,r-shiny)
+ ("r-statmod" ,r-statmod)
+ ("r-zoo" ,r-zoo)))
+ (home-page
+ "http://bioconductor.org/packages/scran")
+ (synopsis
+ "Methods for Single-Cell RNA-Seq Data Analysis")
+ (description
+ "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-scater
+(package
+ (name "r-scater")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "scater" version))
+ (sha256
+ (base32
+ "0pambafir3aqpgk7kdq5i2pn0278d97bn2qb9712c0jivw363whf"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biomart" ,r-biomart)
+ ("r-data-table" ,r-data-table)
+ ("r-dplyr" ,r-dplyr)
+ ("r-edger" ,r-edger)
+ ("r-ggbeeswarm" ,r-ggbeeswarm)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-limma" ,r-limma)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-plyr" ,r-plyr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rhdf5" ,r-rhdf5)
+ ("r-rjson" ,r-rjson)
+ ("r-shiny" ,r-shiny)
+ ("r-shinydashboard" ,r-shinydashboard)
+ ("r-tximport" ,r-tximport)
+ ("r-viridis" ,r-viridis)))
+ (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-rhdf5
+(package
+ (name "r-rhdf5")
+ (version "2.18.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rhdf5" version))
+ (sha256
+ (base32
+ "0pb04li55ysag30s7rap7nnivc0rqmgsmpj43kin0rxdabfn1w0k"))))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'unpack-smallhdf5
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* (
+ (out (assoc-ref %outputs "out"))
+ (name "src/hdf5source/hdf5small.tgz")
+ (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar")))
+ (begin
+ (system* tar "-xzvf" name "-C" "src/" )
+ (substitute* "src/Makevars"
+ (("^.*cd hdf5source &&.*$") "")
+ (("^.*gunzip -dc hdf5small.tgz.*$") "")
+ (("^.*rm -rf hdf5.*$") "")
+ (("^.*mv hdf5source/hdf5 ..*$") ""))
+ (substitute* "src/hdf5/configure"
+ (("/bin/mv") "mv"))
+)
+))))))
+ (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc)))
+ (inputs
+ `(("tar" ,tar)
+ ("perl" ,perl)
+ ("zlib" ,zlib)))
+ (home-page
+ "http://bioconductor.org/packages/rhdf5")
+ (synopsis "HDF5 interface to R")
+ (description
+ "This R/Bioconductor package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.")
+ (license license:artistic2.0)))
+
+(define-public r-tximport
+(package
+ (name "r-tximport")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "tximport" version))
+ (sha256
+ (base32
+ "1k5a7dad6zqg936s17f6cmwgqp11x24z9zhxndsgwbscgpyhpcb0"))))
+ (build-system r-build-system)
+ (home-page
+ "http://bioconductor.org/packages/tximport")
+ (synopsis
+ "Import and summarize transcript-level estimates for gene-level analysis")
+ (description
+ "Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.")
+ (license license:gpl2)))
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index f868da2..20be97e 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3815,3 +3815,159 @@ with alternating row colors) in LaTeX and HTML formats easily from
@code{glm}, @code{coxph}, @code{nls}, @code{fitdistr}, @code{mytable} and
@code{cbind.mytable} objects.")
(license license:gpl2+)))
+
+(define-public r-shiny
+(package
+ (name "r-shiny")
+ (version "0.14.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "shiny" version))
+ (sha256
+ (base32
+ "1sx8c490hbj7lsmvwwq5p4a32dcz4fp4wp1zvaaf2pfg713pk593"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-digest" ,r-digest)
+ ("r-htmltools" ,r-htmltools)
+ ("r-httpuv" ,r-httpuv)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-mime" ,r-mime)
+ ("r-r6" ,r-r6)
+ ("r-sourcetools" ,r-sourcetools)
+ ("r-xtable" ,r-xtable)))
+ (home-page "http://shiny.rstudio.com")
+ (synopsis "Web Application Framework for R")
+ (description
+ "Makes it incredibly easy to build interactive web applications with R. Automatic \"reactive\" binding between inputs and outputs and extensive pre-built widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.")
+ (license license:gpl3)))
+
+(define-public r-statmod
+(package
+ (name "r-statmod")
+ (version "1.4.27")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "statmod" version))
+ (sha256
+ (base32
+ "14yilq9d3z20hig4rs8bjqyydw3dfx90mhmzvw9w8p16h0s595sn"))))
+ (build-system r-build-system)
+ (home-page
+ "http://cran.r-project.org/web/packages/statmod")
+ (inputs
+ `(;; We need not only cairo here, but pango to ensure that tests for the
+ ;; "cairo" bitmapType plotting backend succeed.
+ ("gfortran" ,gfortran)))
+ (synopsis "Statistical Modeling")
+ (description
+ "This package provides a collection of algorithms and functions to aid statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.")
+ (license license:gpl3)))
+
+(define-public r-ggbeeswarm
+(package
+ (name "r-ggbeeswarm")
+ (version "0.5.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ggbeeswarm" version))
+ (sha256
+ (base32
+ "1jgp55rvmzc4agcrlsjn8m5lk85di9c4wj94xzikqkql4lvq3qpd"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-beeswarm" ,r-beeswarm)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-vipor" ,r-vipor)))
+ (home-page
+ "https://github.com/eclarke/ggbeeswarm")
+ (synopsis
+ "Categorical Scatter (Violin Point) Plots")
+ (description
+ "Provides two methods of plotting categorical scatter plots such that the arrangement of points within a category reflects the density of data at that region, and avoids over-plotting.")
+ (license license:gpl2+)))
+
+(define-public r-shinydashboard
+(package
+ (name "r-shinydashboard")
+ (version "0.5.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "shinydashboard" version))
+ (sha256
+ (base32
+ "0anw22qxbis69zm0ls6alsc3ann27hvgs5mv1wvr4ppk7q8cg4l2"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-htmltools" ,r-htmltools)
+ ("r-shiny" ,r-shiny)))
+ (home-page
+ "http://rstudio.github.io/shinydashboard/")
+ (synopsis "Create Dashboards with 'Shiny'")
+ (description
+ "Create dashboards with 'Shiny'. This package provides a theme on top of 'Shiny', making it easy to create attractive dashboards.")
+ (license license:gpl2)))
+
+(define-public r-sourcetools
+(package
+ (name "r-sourcetools")
+ (version "0.1.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "sourcetools" version))
+ (sha256
+ (base32
+ "0jx6kslygfqaic3cmjwag3dy98q1a2dw20cz7z8agsknmmbk6dy2"))))
+ (build-system r-build-system)
+ (home-page
+ "http://cran.r-project.org/web/packages/sourcetools")
+ (synopsis
+ "Tools for Reading, Tokenizing and Parsing R Code")
+ (description
+ "Tools for the reading and tokenization of R code. The 'sourcetools' package provides both an R and C++ interface for the tokenization of R code, and helpers for interacting with the tokenized representation of R code.")
+ (license license:expat)))
+
+(define-public r-beeswarm
+(package
+ (name "r-beeswarm")
+ (version "0.2.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "beeswarm" version))
+ (sha256
+ (base32
+ "0hy89bwv7jixlg91li1fywa77916am2whqp1m1fx1khd45g44581"))))
+ (build-system r-build-system)
+ (home-page
+ "http://www.cbs.dtu.dk/~eklund/beeswarm/")
+ (synopsis
+ "The Bee Swarm Plot, an Alternative to Stripchart")
+ (description
+ "The bee swarm plot is a one-dimensional scatter plot like \"stripchart\", but with closely-packed, non-overlapping points.")
+ (license license:artistic2.0)))
+
+(define-public r-vipor
+(package
+ (name "r-vipor")
+ (version "0.4.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "vipor" version))
+ (sha256
+ (base32
+ "0p1z9a3fazl78pj8a1i2n62v8hrs8cinq82j9wpawhmfkn3dggss"))))
+ (build-system r-build-system)
+ (home-page
+ "http://cran.r-project.org/web/packages/vipor")
+ (synopsis
+ "Plot Categorical Data Using Quasirandom Noise and Density Estimates")
+ (description
+ "Generate a violin point plot, a combination of a violin/histogram plot and a scatter plot by offsetting points within a category based on their density using quasirandom noise.")
+ (license license:gpl2+)))
--
1.9.1
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next reply other threads:[~2016-12-27 9:14 UTC|newest]
Thread overview: 9+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-12-27 9:14 Ra [this message]
2016-12-27 16:02 ` [PATCH] Add r-scran 1.2.0 and all its dependencies Ricardo Wurmus
2016-12-27 16:34 ` Ra
2016-12-27 16:59 ` Ricardo Wurmus
2016-12-27 17:06 ` Ra
2016-12-27 21:25 ` Ra
2016-12-28 9:26 ` Ra
2016-12-29 21:52 ` Ricardo Wurmus
2017-01-31 21:47 ` Ricardo Wurmus
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