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Commit 42460129 authored by Valentin Vautrot's avatar Valentin Vautrot
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Modify .def file to make leafcutter installation work

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leafcutter.def
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......@@ -3,6 +3,7 @@ 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
run the command 'singularity test <image_name>.sif' to see the actual versions of the programms installed.
Authors : valentin.vautrot@u-bourgogne.fr
......@@ -27,142 +28,65 @@ 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-4.0.0 to avoid problems with compilation AND distributional package during R compil
# cf https://github.com/davidaknowles/leafcutter/issues/252
wget -P /usr/bin/ https://cran.r-project.org/src/base/R-4/R-4.0.0.tar.gz
tar -xzvf /usr/bin/R-4.0.0.tar.gz -C /usr/bin/
cd /usr/bin/R-4.0.0
# 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
# 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
./configure
make
# export PATH=${PATH}:/usr/bin/R-3.6.0/bin/
export PATH=${PATH}:/usr/bin/R-4.0.0/bin/
# export PATH=${PATH}:/usr/bin/R-4.4.2/bin/
export PATH=${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 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("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 Rv4.0.0
Rscript -e 'install.packages("devtools", repos="https://cran.r-project.org")'
Rscript -e 'install.packages("BiocManager", dependencies=TRUE, repos="https://cran.r-project.org")'
# # install leafcutter for Rv4.3.0
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
Rscript -e 'BiocManager::install("DirichletMultinomial", version="3.12")'
Rscript -e 'BiocManager::install("Biobase", version="3.12")'
# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/rstan/rstan_2.26.23.tar.gz")'
# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/rstantools/rstantools_2.3.1.tar.gz")'
Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/htmlTable/htmlTable_1.13.3.tar.gz")'
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")'
pip2 install --upgrade -t /usr/lib/python2.7/site-packages/ tbb==2021.13.1
# Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/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 'devtools::install_github("davidaknowles/leafcutter/leafcutter", ref="psi_2019")'
# # # 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 'install.packages("https://cran.r-project.org/src/contrib/Archive/StanHeaders/StanHeaders_2.32.9.tar.gz")'
# Rscript -e 'devtools::install_github("davidaknowles/leafcutter/leafcutter")'
Rscript -e 'BiocManager::install("DirichletMultinomial", version="3.18")'
Rscript -e 'BiocManager::install("Biobase", version="3.18")'
Rscript -e 'install.packages("BH", version="1.87.0-1", repos="https://cran.r-project.org")'
Rscript -e 'install.packages("RcppEigen", version="0.3.4.0.2", repos="https://cran.r-project.org")'
Rscript -e 'install.packages("loo", version="2.8.0", repos="https://cran.r-project.org")'
Rscript -e 'install.packages("RcppParallel", version="5.1.10", repos="https://cran.r-project.org")'
Rscript -e 'install.packages("gridExtra", version="2.3", repos="https://cran.r-project.org")'
Rscript -e 'install.packages("inline", version="0.3.21", 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("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.
Rscript -e 'devtools::install_github("davidaknowles/leafcutter/leafcutter", upgrade="never")'
mkdir /usr/bin/leafcutter/
git clone https://github.com/davidaknowles/leafcutter /usr/bin/leafcutter/
cd /usr/bin/leafcutter/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=${PATH}:/usr/bin/regtools/build/
# install samtools and regtools
dnf install -y samtools
dnf install -y cmake.x86_64
mkdir /usr/bin/regtools/
git clone https://github.com/griffithlab/regtools /usr/bin/regtools/
mkdir /usr/bin/regtools/build/
cd /usr/bin/regtools/build/
cmake ..
make
%environment
# export PATH=${PATH}:/usr/bin/regtools/build/:/usr/bin/R-3.6.0/bin/
export PATH=${PATH}:/usr/bin/regtools/build/:/usr/bin/R-4.0.0/bin/
# %test
# echo "installed python version"
# python2 --version
# echo "installed R version:"
# R --version
# echo "installed samtools version:"
# samtools --version
# echo "installed regtools version:"
# regtools --help
\ No newline at end of file
export PATH=${PATH}:/usr/bin/regtools/build/:/usr/bin/R-4.3.0/bin/
export LEAFCUTTERDIR=/usr/bin/leafcutter/
%test
echo "\n##### installed python version"
python2 --version
echo "\n\n##### installed R version:"
R --version
echo "\n\n##### installed samtools version:"
samtools --version
echo "\n\n##### installed regtools version:"
regtools --help
echo "\n\n##### installed perl version:"
perl --version
echo "\n\n##### leafcutter version: "
echo "leafcutter $(grep "^Version: " ${LEAFCUTTERDIR}/leafcutter/DESCRIPTION)"
\ No newline at end of file
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