Add polyRAD

.github/workflows/R-CMD-check.yaml

@@ -22,7 +22,6 @@ jobs:
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

DESCRIPTION

@@ -27,6 +27,7 @@ License: Apache License (== 2.0)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
+Depends: R (>= 4.4.0)
 biocViews:
 Imports: 
     vcfR (>= 1.15.0),
@@ -35,6 +36,8 @@ Imports:
     DT,
     dplyr,
     bs4Dash,
+    polyRAD,
+    R.utils,
     golem,
     ggplot2,
     purrr,
@@ -62,9 +65,11 @@ Imports:
     config,
     Matrix,
     matrixcalc,
-    markdown
+    markdown,
+    Rsamtools
 Remotes:
     github::jendelman/GWASpoly,
-    github::Breeding-Insight/BIGr
+    github::Breeding-Insight/BIGr,
+    bioc::Rsamtools
 Suggests:
     testthat

Dockerfile

@@ -0,0 +1,47 @@
+FROM rocker/r-ver:4.4.2
+RUN apt-get update && apt-get install -y  cmake libz-dev libcurl4-openssl-dev libssl-dev
+RUN R -e 'install.packages("remotes")'
+RUN Rscript -e 'remotes::install_version("adegenet",upgrade="never", version = "2.1.10")'
+RUN Rscript -e 'remotes::install_version("curl",upgrade="never", version = "6.0.1")'
+RUN Rscript -e 'remotes::install_version("DT",upgrade="never", version = "0.33")'
+RUN Rscript -e 'remotes::install_version("dplyr",upgrade="never", version = "1.1.4")'
+RUN Rscript -e 'remotes::install_version("vcfR",upgrade="never", version = "1.15.0")'
+RUN Rscript -e 'remotes::install_version("ggplot2",upgrade="never", version = "3.5.1")'
+RUN Rscript -e 'remotes::install_version("tidyr",upgrade="never", version = "1.3.1")'
+RUN Rscript -e 'remotes::install_version("curl",upgrade="never", version = "6.0.1")'
+RUN Rscript -e 'remotes::install_version("shiny",upgrade="never", version = "1.9.1")'
+RUN Rscript -e 'remotes::install_version("config",upgrade="never", version = "0.3.2")'
+RUN Rscript -e 'remotes::install_version("bs4Dash",upgrade="never", version = "2.3.4")'
+RUN Rscript -e 'remotes::install_version("golem",upgrade="never", version = "0.5.1")'
+RUN Rscript -e 'remotes::install_version("purrr",upgrade="never", version = "1.0.2")'
+RUN Rscript -e 'remotes::install_version("markdown",upgrade="never", version = "1.13")'
+RUN Rscript -e 'remotes::install_version("scales",upgrade="never", version = "1.3.0")'
+RUN Rscript -e 'remotes::install_version("plotly",upgrade="never", version = "4.10.4")'
+RUN Rscript -e 'remotes::install_version("shinyWidgets",upgrade="never", version = "0.8.7")'
+RUN Rscript -e 'remotes::install_version("shinyjs",upgrade="never", version = "2.1.0")'
+RUN Rscript -e 'remotes::install_version("shinydisconnect",upgrade="never", version = "0.1.1")'
+RUN Rscript -e 'remotes::install_version("shinyalert",upgrade="never", version = "3.1.0")'
+RUN Rscript -e 'remotes::install_version("stringr",upgrade="never", version = "1.5.1")'
+RUN Rscript -e 'remotes::install_version("updog",upgrade="never", version = "2.1.5")'
+RUN Rscript -e 'remotes::install_version("AGHmatrix",upgrade="never", version = "2.1.4")'
+RUN Rscript -e 'remotes::install_version("factoextra",upgrade="never", version = "1.0.7")'
+RUN Rscript -e 'remotes::install_version("httr",upgrade="never", version = "1.4.7")'
+RUN Rscript -e 'remotes::install_version("future",upgrade="never", version = "1.34.0")'
+RUN Rscript -e 'remotes::install_version("shinycssloaders",upgrade="never", version = "1.1.0")'
+RUN Rscript -e 'remotes::install_version("RColorBrewer",upgrade="never", version = "1.1.3")'
+RUN Rscript -e 'remotes::install_version("tibble",upgrade="never", version = "3.2.1")'
+RUN Rscript -e 'remotes::install_version("rrBLUP",upgrade="never", version = "4.6.3")'
+RUN Rscript -e 'remotes::install_version("MASS",upgrade="never", version = "7.3.60.2")'
+RUN Rscript -e 'remotes::install_version("Matrix",upgrade="never", version = "1.7.0")'
+RUN Rscript -e 'remotes::install_version("matrixcalc",upgrade="never", version = "1.0.6")'
+RUN Rscript -e 'remotes::install_github("Breeding-Insight/BIGr",upgrade="never")'
+RUN Rscript -e 'remotes::install_github("jendelman/GWASpoly",upgrade="never")'
+
+RUN mkdir /build_zone
+ADD . /build_zone
+WORKDIR /build_zone
+RUN R -e 'remotes::install_local(upgrade="never")'
+RUN rm -rf /build_zone
+EXPOSE 80
+CMD R -e "options('shiny.port'=80,shiny.host='0.0.0.0');BIGapp::run_app()"
+

NAMESPACE

@@ -6,9 +6,12 @@ import(GWASpoly)
 import(dplyr)
 import(ggplot2)
 import(grDevices)
+import(polyRAD)
 import(rrBLUP)
 import(shiny)
 import(shinyWidgets)
+import(shinydisconnect)
+import(tibble)
 import(tidyr)
 import(updog)
 import(utils)
@@ -17,13 +20,16 @@ importClassesFrom(adegenet,genlight)
 importFrom(AGHmatrix,Amatrix)
 importFrom(AGHmatrix,Gmatrix)
 importFrom(AGHmatrix,Hmatrix)
+importFrom(BIGr,flip_dosage)
 importFrom(BIGr,updog2vcf)
 importFrom(DT,DTOutput)
 importFrom(DT,datatable)
 importFrom(DT,renderDT)
 importFrom(MASS,ginv)
 importFrom(Matrix,nearPD)
+importFrom(R.utils,gunzip)
 importFrom(RColorBrewer,brewer.pal)
+importFrom(Rsamtools,bgzip)
 importFrom(adegenet,"pop<-")
 importFrom(adegenet,dapc)
 importFrom(adegenet,find.clusters)
@@ -124,4 +130,6 @@ importFrom(stats,setNames)
 importFrom(stringr,str_split)
 importFrom(tibble,rownames_to_column)
 importFrom(vcfR,extract.gt)
+importFrom(vcfR,is.biallelic)
 importFrom(vcfR,read.vcfR)
+importFrom(vcfR,write.vcf)