Add test section, labels, clean-up and annotations

R_3.6_outrider.def

@@ -4,17 +4,10 @@ From: ubuntu:18.04
 %help 
 This is a singularity container packing R version 3.6.3 and all the dependencies necessary to run the outrider ("Outlier in rnaseq finder") package, version 1.4.2, for rnaseq analysis.
 (BiocManager version : 3.10)
+built-in R packages are installed in /usr/lib/R/library
+other R packages were added in /usr/local/lib/R/site-library
 Authors : valentin.vautrot@u-bourgogne.fr
 
-%apprun R
-  exec R "${@}"
-
-%apprun Rscript
-  exec Rscript "${@}"
-
-%runscript
-  exec R "${@}"
-
 %post
 
 export R_VERSION=3.6.3
@@ -30,17 +23,13 @@ apt-get install -y --no-install-recommends \
     wget \
 
 wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
-# add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/"
 add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/"
 apt update
 
 apt-get install -y --no-install-recommends -t bionic-cran35 r-base=${R_VERSION}-1bionic r-recommended=${R_VERSION}-1bionic r-base-core=${R_VERSION}-1bionic r-base-dev=${R_VERSION}-1bionic r-base-html=${R_VERSION}-1bionic r-doc-html=${R_VERSION}-1bionic
 
 apt-get install -y --no-install-recommends libcurl4-openssl-dev libxml2-dev libssl-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev
-    # libcairo2-dev \
-    # libxt-dev \
-    # libopenblas-dev
-   
+
 # # Add a directory for host R libraries
 # mkdir -p /library
 # echo "R_LIBS_SITE=/library:\${R_LIBS_SITE}" >> /usr/lib/R/etc/Renviron.site
@@ -54,8 +43,16 @@ Rscript -e 'devtools::install_version("Hmisc", version ="4.3.0", repos = "https:
 Rscript -e 'install.packages("BiocManager", dependencies=TRUE)'
 Rscript -e 'BiocManager::install("OUTRIDER", version = "3.10")'
 
-# # Clean up
-# rm -rf /var/lib/apt/lists/*
+# Clean up
+rm -rf /var/lib/apt/lists/*
+
+%test
+echo "installed R version :"
+R --version
+echo "installed OUTRIDER package version :"
+Rscript -e 'packageVersion("OUTRIDER")'
 
-# %test
-# R --quiet -e "stopifnot(getRversion() == '${R_VERSION}')"
\ No newline at end of file
+%labels 
+Contained_OS_version Ubuntu_18.04_LTS_BionicBeaver
+Contained_R_version 3.6.3
+Contained_OUTRIDER_version 1.4.2
\ No newline at end of file