Add draft of leafcutter singularity definition file

leafcutter.def

+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.
+run the command 'singularity test <image_name>.sif' to see the actual versions of the programms installed.
+Authors : valentin.vautrot@u-bourgogne.fr
+
+%post
+sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
+sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-*
+
+dnf install -y epel-release
+dnf update -y libmodulemd
+dnf update -y --exclude=filesystem
+# 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
+
+# install R
+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 
+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-3.6.0
+wget -P /usr/bin/ https://cran.r-project.org/src/base/R-3/R-3.6.0.tar.gz
+tar -xzvf /usr/bin/R-3.6.0.tar.gz -C /usr/bin/
+cd /usr/bin/R-3.6.0
+
+# install R-4.2.1 to avoid problems with tbb AND distributional package during R compil
+wget -P /usr/bin/ https://cran.r-project.org/src/base/R-4/R-4.2.1.tar.gz
+tar -xzvf /usr/bin/R-4.2.1.tar.gz -C /usr/bin/
+cd /usr/bin/R-4.2.1
+
+
+#  install R-4.4.2
+# wget -P /usr/bin/ https://cran.r-project.org/src/base/R-4/R-4.4.2.tar.gz
+# tar -xzvf /usr/bin/R-4.4.2.tar.gz -C /usr/bin/
+# cd /usr/bin/R-4.4.2
+
+./configure
+make
+export PATH=${PATH}:/usr/bin/R-3.6.0/bin/
+export PATH=${PATH}:/usr/bin/R-4.2.1/bin/
+# export PATH=${PATH}:/usr/bin/R-4.4.2/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 devtools for R 3.6.0
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/httr2/httr2_1.0.1.tar.gz")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/diffobj/diffobj_0.3.4.tar.gz")'
+# Rscript -e 'install.packages("tibble", version="3.2.1", repos="https://cran.r-project.org")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/rematch2/rematch2_2.1.1.tar.gz")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/waldo/waldo_0.5.3.tar.gz")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/purrr/purrr_1.0.2.tar.gz")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/cpp11/cpp11_0.5.0.tar.gz")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/downlit/downlit_0.4.3.tar.gz")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/systemfonts/systemfonts_1.0.5.tar.gz")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/textshaping/textshaping_0.3.7.tar.gz")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/ragg/ragg_1.3.2.tar.gz")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/tinytex/tinytex_0.48.tar.gz")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/rmarkdown/rmarkdown_2.28.tar.gz")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/htmlwidgets/htmlwidgets_1.6.3.tar.gz")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/pkgdown/pkgdown_2.1.0.tar.gz")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/profvis/profvis_0.3.8.tar.gz")'
+# Rscript -e 'install.packages("devtools", version="2.4.5", repos="https://cran.r-project.org")'
+# # install leafcutter for R 3.6.0
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/00Archive/gtable/gtable_0.3.5.tar.gz")'
+# # Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/00Archive/scales/scales_1.2.1.tar.gz")'
+# # Rscript -e 'install.packages("generics", version="0.1.3", repos="https://cran.r-project.org")'
+# # Rscript -e 'install.packages("farver", version="0.1.3", repos="https://cran.r-project.org")'
+# # Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/00Archive/farver/farver_2.1.1.tar.gz")'
+# # Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/00Archive/ggplot2/ggplot2_3.4.4.tar.gz")'
+# # Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/00Archive/numDeriv/numDeriv_2016.8-1.tar.gz")'
+# Rscript -e 'install.packages("scales", version = "1.3.0", repos = "https://cran.r-project.org")'
+# Rscript -e 'install.packages("ggplot2", version = "3.5.1", repos = "https://cran.r-project.org")'
+# Rscript -e 'install.packages("distributional", version = "0.5.0", repos = "https://cran.r-project.org")'
+# # Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/00Archive/distributional/distributional_0.5.0.tar.gz")'
+# Rscript -e 'install.packages("rstan", version="2.32.6", repos = "https://cran.r-project.org")'
+# Rscript -e 'install.packages("rstantools", version="2.4.0", 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
+# Rscript -e 'BiocManager::install("DirichletMultinomial", version="3.10")'
+# Rscript -e 'BiocManager::install("Biobase", version="3.10")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/htmlTable/htmlTable_1.13.3.tar.gz")'
+# Rscript -e 'install.packages("rstantools", version="2.4.0", repos = "https://cran.r-project.org")'
+# Rscript -e 'install.packages("data.table", version = "1.16.4, repos = "https://cran.r-project.org")'
+# Rscript -e 'install.packages("viridis", version = 0.6.5, repos = "https://cran.r-project.org")'
+# Rscript -e 'install.packages("Formula", version = "1.2-5", repos = "https://cran.r-project.org")'
+# Rscript -e 'install.packages("latticeExtra", version = "0.6-30", repos = "https://cran.r-project.org")'
+# Rscript -e 'install.packages("acepack", version = "1.5.2", repos = "https://cran.r-project.org")'
+# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/Hmisc/Hmisc_4.3-0.tar.gz")'
+# Rscript -e 'devtools::install_github("davidaknowles/leafcutter/leafcutter")'
+
+# # install leafcutter for Rv4.2.1
+Rscript -e 'install.packages("devtools", repos="https://cran.r-project.org")'
+Rscript -e 'install.packages("BiocManager", dependencies=TRUE, repos="https://cran.r-project.org")'
+# dnf install -y gsl.x86_64 gsl-devel.x86_64 tbb.x86_64 tbb-devel.x86_64
+Rscript -e 'BiocManager::install("DirichletMultinomial", version="3.16")'
+Rscript -e 'BiocManager::install("Biobase", version="3.16")'
+Rscript -e 'install.packages("rstan", repos = "https://cran.r-project.org")'
+Rscript -e 'install.packages("rstantools", repos = "https://cran.r-project.org")'
+# trying to change rstan version to avoid compilation bugs with tbb
+# 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_2.2.0.tar.gz")'
+Rscript -e 'devtools::install_github("davidaknowles/leafcutter/leafcutter")'
+
+
+# # # install leafcutter for Rv4.4.2
+# Rscript -e 'install.packages("devtools", version="2.4.5", repos="https://cran.r-project.org")'
+# Rscript -e 'install.packages("BiocManager", dependencies=TRUE, repos="https://cran.r-project.org")'
+# dnf install -y gsl.x86_64 gsl-devel.x86_64 tbb.x86_64 tbb-devel.x86_64
+# Rscript -e 'BiocManager::install("DirichletMultinomial", version="3.20")'
+# Rscript -e 'BiocManager::install("Biobase", version="3.20")'
+# Rscript -e 'install.packages("rstan", version="2.32.6", repos = "https://cran.r-project.org")'
+# Rscript -e 'install.packages("rstantools", version="2.4.0", repos = "https://cran.r-project.org")'
+# # trying to change rstan version to avoid compilation bugs with tbb
+# # 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_2.2.0.tar.gz")'
+# Rscript -e 'devtools::install_github("davidaknowles/leafcutter/leafcutter")'
+
+# mkdir /usr/bin/leafcutter/
+# git clone https://github.com/davidaknowles/leafcutter /usr/bin/leafcutter/
+
+# # install samtools and regtools
+# dnf install -y samtools
+# 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/
+# cd /usr/bin/regtools/build/
+# cmake ..
+# make
+# export PATH=${PATH}:/usr/bin/regtools/build/
+
+# %environment
+# export PATH=${PATH}:/usr/bin/regtools/build/:/usr/bin/R_3.6.0
+
+# %test
+# echo "installed python version"
+# python2 --version
+# echo "installed R version:"
+# R --version
+# echo "installed samtools version:"
+# samtools --version
+# echo "installed regtools version:"
+# regtools --help
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