Replace affy package with oligo and add limma

R_4.4.0_affymetrix.def

@@ -2,8 +2,8 @@ BootStrap: docker
 From: ubuntu:22.04
 
 %help 
-This is a singularity container packing R version 4.4.0 and all the dependencies necessary to run the affy package from affymetrix, in order to process .cel transcriptomics files
-run the command 'apptainer test <image_name>.sif' to see the actual versions of R and "affy" package installed
+This is a singularity container packing R version 4.4.0 and all the dependencies necessary to run the oligo and limma packages for microarray data treatment, in order to process .cel transcriptomics files from mouse.
+Run the command 'apptainer test <image_name>.sif' to see the actual versions of R and other packages installed.
 built-in R packages should be located in /usr/lib/R/library
 other R packages should be located in /usr/local/lib/R/site-library
 Authors : valentin.vautrot@u-bourgogne.fr
@@ -29,10 +29,11 @@ echo "installed R version :"
 R --version
 
 # # install R packages :
-# Rscript -e 'install.packages("devtools")'
 Rscript -e 'install.packages("BiocManager", dependencies=TRUE)'
 Rscript -e 'BiocManager::install("Biobase", version = "3.19")'
-Rscript -e 'BiocManager::install("affy", version = "3.19")'
+Rscript -e 'BiocManager::install("oligo", version = "3.19")'
+Rscript -e 'BiocManager::install("pd.clariom.s.mouse", version = "3.19")'
+Rscript -e 'BiocManager::install("limma", version = "3.19")'
 
 # Clean up
 rm -rf /var/lib/apt/lists/*
@@ -46,11 +47,14 @@ export LC_CTYPE=fr_FR.UTF-8
 %test
 echo "installed R version :"
 R --version
-echo "installed affy package version :"
-Rscript -e 'packageVersion("affy")'
+echo "installed oligo package version :"
+Rscript -e 'packageVersion("oligo")'
+echo "annotation package pd.clariom.s.mouse :"
+Rscript -e 'packageVersion("pd.clariom.s.mouse")'
+echo "installed limma version :"
+Rscript -e 'packageVersion("limma")'
 
 %labels 
 Auhtors valentin.vautrot@u-bourgogne.fr
 Contained_OS_version Ubuntu_22.04_LTS_JammyJellyfish
-Contained_R_version 4.4.0
-Contained_FRASER_version 1.14.1
\ No newline at end of file
+Contained_R_version 4.4.0
\ No newline at end of file