Singularity_recipe_4.0.3_libraries

BootStrap: shub
From: shub://elisadonnard/singularity:0.3

%labels

    AUTHOR Elisa Donnard
    Version v1

%apprun R
exec R "$@"

%apprun Rscript
exec Rscript "$@"

%runscript
exec R "$@"

%post  
  R --version
  
  # installing packages from cran
  R --slave -e 'install.packages("devtools",repos="https://cran.rstudio.com/")'
  R --slave -e 'install.packages("BiocManager",repos="https://cran.rstudio.com/")'
  R --slave -e 'install.packages("Seurat",repos="https://cran.rstudio.com/")'

  # installing from bioc
  R --slave -e 'if (!requireNamespace("BiocManager",quietly=TRUE)) install.packages("BiocManager")'
  R --slave -e 'BiocManager::install()'
  R --slave -e 'BiocManager::install("tximport",ask=FALSE)'
  R --slave -e 'BiocManager::install("biomaRt",ask=FALSE)'
  R --slave -e 'BiocManager::install("DESeq2",ask=FALSE)'
  R --slave -e 'BiocManager::install("tidyverse")'
  R --slave -e 'BiocManager::install("edgeR")'
  R --slave -e 'BiocManager::install("gplots")'
  R --slave -e 'BiocManager::install("Biobase", dep = TRUE)'
  R --slave -e 'BiocManager::install("DropletUtils", dep = TRUE)'
  R --slave -e 'BiocManager::install("stringr", dep = TRUE)'
  R --slave -e 'BiocManager::install("densityClust", dep = TRUE)'
  R --slave -e 'BiocManager::install("RColorBrewer", dep = TRUE)'
  R --slave -e 'BiocManager::install("Rtsne", dep = TRUE)'
  R --slave -e 'BiocManager::install("ggpubr", dep = TRUE)'
  R --slave -e 'BiocManager::install("limSolve", dep = TRUE)'
  R --slave -e 'BiocManager::install("scran", dep = TRUE)'
  R --slave -e 'BiocManager::install("fpc", dep = TRUE)'
  R --slave -e 'BiocManager::install("irlba", dep = TRUE)'
  
 
###################
# mount directories

mkdir /seq