Singularity_recipe_scenic

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

%labels

    AUTHOR Elisa Donnard
    Version v1

%apprun R
exec R "$@"

%apprun Rscript
exec Rscript "$@"

%runscript
exec R "$@"

%post  
  R --version
  
  R --slave -e 'BiocManager::install("AUCell")'
  R --slave -e 'BiocManager::install("RcisTarget")'
  R --slave -e 'BiocManager::install("GENIE3")' 
  R --slave -e 'BiocManager::install(c("zoo", "mixtools", "rbokeh"))'
  R --slave -e 'BiocManager::install(c("DT", "NMF", "ComplexHeatmap", "R2HTML", "Rtsne"))'
  R --slave -e 'BiocManager::install(c("doMC", "doRNG"))'
  R --slave -e 'devtools::install_github("aertslab/SCENIC")'

  R --slave -e 'BiocManager::install("BiocParallel")'
  R --slave -e 'BiocManager::install("data.table")'
  R --slave -e 'BiocManager::install("grid")'
  R --slave -e 'BiocManager::install("ComplexHeatmap")' 

###################
# mount directories

mkdir /seq