Subject: [PATCH] r-signac and r-chromstardata

From: hong li <[email-masked]>
Date: Thu, 18 Mar 2021 01:14:25 +0100

Dear Guixer,

Can you please add these two r packages in guix? Thanks in advance.
I am not sure how to create this patch, and this is what I did:

guix import cran -a git -r 'https://github.com/timoast/signac/'

(define-public r-signac
  (let ((commit
          "e0512d348adeda4a3f23a2e8f56d1fe09840e03c")
        (revision "1"))
    (package
      (name "r-signac")
      (version (git-version "1.1.1" revision commit))
      (source
        (origin
          (method git-fetch)
          (uri (git-reference
                 (url "https://github.com/timoast/signac/")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
            (base32
              "1yihhrv7zs87ax61la1nb4y12lg3knraw4b20k5digbcwm8488lb"))))
      (properties `((upstream-name . "Signac")))
      (build-system r-build-system)
      (inputs `(("zlib" ,zlib)))
      (propagated-inputs
        `(("r-annotationfilter" ,r-annotationfilter)
          ("r-biocgenerics" ,r-biocgenerics)
          ("r-biostrings" ,r-biostrings)
          ("r-biovizbase" ,r-biovizbase)
          ("r-data-table" ,r-data-table)
          ("r-dplyr" ,r-dplyr)
          ("r-fastmatch" ,r-fastmatch)
          ("r-future" ,r-future)
          ("r-future-apply" ,r-future-apply)
          ("r-genomeinfodb" ,r-genomeinfodb)
          ("r-genomicranges" ,r-genomicranges)
          ("r-ggbio" ,r-ggbio)
          ("r-ggforce" ,r-ggforce)
          ("r-ggplot2" ,r-ggplot2)
          ("r-ggrepel" ,r-ggrepel)
          ("r-ggseqlogo" ,r-ggseqlogo)
          ("r-iranges" ,r-iranges)
          ("r-irlba" ,r-irlba)
          ("r-lsa" ,r-lsa)
          ("r-matrix" ,r-matrix)
          ("r-patchwork" ,r-patchwork)
          ("r-pbapply" ,r-pbapply)
          ("r-rcpp" ,r-rcpp)
          ("r-rcpproll" ,r-rcpproll)
          ("r-rsamtools" ,r-rsamtools)
          ("r-s4vectors" ,r-s4vectors)
          ("r-scales" ,r-scales)
          ("r-seurat" ,r-seurat)
          ("r-seuratobject" ,r-seuratobject)
          ("r-stringi" ,r-stringi)
          ("r-tidyr" ,r-tidyr)))
      (home-page "https://github.com/timoast/signac/")
      (synopsis
        "Analysis of Single-Cell Chromatin Data")
      (description
        "This package provides a framework for the analysis and exploration
of single-cell chromatin data.  The 'Signac' package contains functions for
quantifying single-cell chromatin data, computing per-cell quality control
metrics, dimension reduction and normalization, visualization, and DNA
sequence motif analysis.  Reference: Stuart et al. (2020)
<doi:10.1101/2020.11.09.373613>.")
      (license expat))))

guix import cran -a git -r 'https://git.bioconductor.org/packages/chromstaR'

(define-public r-chromstardata
  (package
    (name "r-chromstardata")
    (version "1.16.0")
    (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri
               "chromstaRData"
               version
               'experiment))
        (sha256
          (base32
            "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab"))))
    (properties `((upstream-name . "chromstaRData")))
    (build-system r-build-system)
    (home-page
      "https://bioconductor.org/packages/chromstaRData")
    (synopsis
      "ChIP-seq data for Demonstration Purposes")
    (description
      "ChIP-seq data for demonstration purposes in the chromstaR package.")
    (license gpl3)))

(define-public r-chromstar
  (let ((commit
          "16c0394a3a0857a050237d2b8b33cd02d92d6239")
        (revision "1"))
    (package
      (name "r-chromstar")
      (version (git-version "1.17.0" revision commit))
      (source
        (origin
          (method git-fetch)
          (uri (git-reference
                 (url "https://git.bioconductor.org/packages/chromstaR")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
            (base32
              "0wr6wlz3z3x21c25hgczalswicrqfhw00wmsa9jjd42w4hj5lkh9"))))
      (properties `((upstream-name . "chromstaR")))
      (build-system r-build-system)
      (propagated-inputs
        `(("r-bamsignals" ,r-bamsignals)
          ("r-biocgenerics" ,r-biocgenerics)
          ("r-chromstardata" ,r-chromstardata)
          ("r-doparallel" ,r-doparallel)
          ("r-foreach" ,r-foreach)
          ("r-genomeinfodb" ,r-genomeinfodb)
          ("r-genomicalignments" ,r-genomicalignments)
          ("r-genomicranges" ,r-genomicranges)
          ("r-ggplot2" ,r-ggplot2)
          ("r-iranges" ,r-iranges)
          ("r-mvtnorm" ,r-mvtnorm)
          ("r-reshape2" ,r-reshape2)
          ("r-rsamtools" ,r-rsamtools)
          ("r-s4vectors" ,r-s4vectors)))
      (native-inputs `(("r-knitr" ,r-knitr)))
      (home-page
        "https://git.bioconductor.org/packages/chromstaR")
      (synopsis
        "Combinatorial and Differential Chromatin State Analysis for
ChIP-Seq Data")
      (description
        "This package implements functions for combinatorial and
differential analysis of ChIP-seq data.  It includes uni- and multivariate
peak-calling, export to genome browser viewable files, and functi
ons for enrichment analyses.")
      (license artistic2.0))))

with best regards,
Hong Li