Complete %test and %help section and reorganize building script

leafcutter.def

@@ -2,10 +2,14 @@ Bootstrap: docker
 From: centos:8
 
 %help 
-This is a singularity container packing a python 2.7 (only version) environment with all the programms necessary to execute the leafcutter software for RNA splicing. These include samtools, regtools and R3.6.0.
-Leafcutter is installed in /usr/bin/leafcutter
+This is a singularity container packing an environment with all programs necessary to execute the leafcutter software for RNA splicing. These include python2.7, samtools, regtools, and perl.
 run the command 'singularity test <image_name>.sif' to see the actual versions of the programms installed.
+
+This image requires that a copy of the leafcutter git directory is available on the host environment to acess leafcutter scripts folders.
+Usage : singularity exec -e <image_name>.sif python2/perl/Rscript depending on the leafcutter scripts used.
+
 Authors : valentin.vautrot@u-bourgogne.fr
+Creation date : 2025-02-14
 
 %post
 sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
@@ -14,13 +18,15 @@ sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /
 dnf install -y epel-release
 dnf update -y libmodulemd
 dnf update -y --exclude=filesystem
+dnf install -y git
 # filesystem packages updates poses problems by tempering with /proc, which is supposed to be owned by root, but is not in the .sif image
 
 # install python2.7
 dnf remove -y python && dnf autoremove
-dnf install -y python2.x86_64 git
+dnf install -y python2.x86_64
 
-# install R
+# install R-4.3.0 to avoid problems with compilation AND distributional package during R compil
+# cf also https://github.com/davidaknowles/leafcutter/issues/239
 dnf install -y wget gcc gcc-gfortran gcc-c++ kernel-devel readline-devel.x86_64 
 dnf install -y xorg-x11-server-utils.x86_64 libX11-devel.x86_64 libXt-devel.x86_64
 dnf install -y zlib-devel.x86_64 bzip2.x86_64 bzip2-devel.x86_64 xz-devel.x86_64 pcre-devel.x86_64 libcurl-devel.x86_64 
@@ -28,8 +34,6 @@ dnf install -y make java-1.8.0-openjdk.x86_64
 # for R > 4 only
 dnf install -y pcre2.x86_64 pcre2-devel.x86_64
 
-# install R-4.3.0 to avoid problems with compilation AND distributional package during R compil
-# cf also https://github.com/davidaknowles/leafcutter/issues/239
 wget -P /usr/bin/ https://cran.r-project.org/src/base/R-4/R-4.3.0.tar.gz
 tar -xzvf /usr/bin/R-4.3.0.tar.gz -C /usr/bin/
 cd /usr/bin/R-4.3.0
@@ -39,9 +43,8 @@ make
 export PATH=${PATH}:/usr/bin/R-4.3.0/bin/
 cd
 
-dnf install -y openssl-devel.x86_64 libxml2-devel.x86_64 fontconfig-devel.x86_64 harfbuzz-devel fribidi-devel freetype-devel libpng-devel libtiff-devel libjpeg-devel
-
 # # install leafcutter for Rv4.3.0
+dnf install -y openssl-devel.x86_64 libxml2-devel.x86_64 fontconfig-devel.x86_64 harfbuzz-devel fribidi-devel freetype-devel libpng-devel libtiff-devel libjpeg-devel
 Rscript -e 'install.packages("devtools", version="2.4.5", repos="https://cran.r-project.org")'
 Rscript -e 'install.packages("BiocManager", version="1.30.25", repos="https://cran.r-project.org")'
 dnf install -y gsl.x86_64 gsl-devel.x86_64 tbb.x86_64 tbb-devel.x86_64
@@ -57,7 +60,7 @@ Rscript -e 'install.packages("ggplot2", version="3.5.1", repos="https://cran.r-p
 Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/StanHeaders/StanHeaders_2.21.0-7.tar.gz")'
 Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/rstan/rstan_2.21.7.tar.gz")'
 Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/rstantools/rstantools_2.0.0.tar.gz")'
-# fail then  reinstall the 3 stan packages then try with upgrade = "never") - probably because upgrading StanHeaders causes failure.
+#  upgrade = "never" mandatory - probably because upgrading StanHeaders causes failure.
 Rscript -e 'devtools::install_github("davidaknowles/leafcutter/leafcutter", upgrade="never")'
 
 mkdir /usr/bin/leafcutter/
@@ -65,7 +68,7 @@ git clone https://github.com/davidaknowles/leafcutter /usr/bin/leafcutter/
 
 # install samtools and regtools
 dnf install -y samtools
-dnf install -y cmake.x86_64 
+dnf install -y cmake.x86_64
 mkdir /usr/bin/regtools/
 git clone https://github.com/griffithlab/regtools /usr/bin/regtools/
 mkdir /usr/bin/regtools/build/
@@ -78,15 +81,15 @@ export PATH=${PATH}:/usr/bin/regtools/build/:/usr/bin/R-4.3.0/bin/
 export LEAFCUTTERDIR=/usr/bin/leafcutter/
 
 %test
-echo "\n##### installed python version"
+echo "##### installed python version"
 python2 --version
-echo "\n\n##### installed R version:"
+echo "##### installed R version:"
 R --version
-echo "\n\n##### installed samtools version:"
+echo "##### installed samtools version:"
 samtools --version
-echo "\n\n##### installed regtools version:"
+echo "##### installed regtools version:"
 regtools --help
-echo "\n\n##### installed perl version:"
+echo "##### installed perl version:"
 perl --version
-echo "\n\n##### leafcutter version: "
+echo "\n\n##### installed leafcutter version: "
 echo "leafcutter $(grep "^Version: " ${LEAFCUTTERDIR}/leafcutter/DESCRIPTION)"
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