Skip to content

S
singularity
Commit 176e6f89 authored by Valentin Vautrot's avatar Valentin Vautrot
Browse files
Options

Save draft for R install trys

parent 8ea2c946
Hide whitespace changes
Inline Side-by-side
Showing with 42 additions and 27 deletions
leafcutter.def
View file @ 176e6f89
......@@ -28,14 +28,15 @@ dnf install -y make java-1.8.0-openjdk.x86_64
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
# 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-4.0.0 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
......@@ -45,8 +46,8 @@ cd /usr/bin/R-4.2.1
./configure
make
export PATH=${PATH}:/usr/bin/R-3.6.0/bin/
export PATH=${PATH}:/usr/bin/R-4.2.1/bin/
# export PATH=${PATH}:/usr/bin/R-3.6.0/bin/
export PATH=${PATH}:/usr/bin/R-4.0.0/bin/
# export PATH=${PATH}:/usr/bin/R-4.4.2/bin/
cd
......@@ -89,28 +90,39 @@ dnf install -y openssl-devel.x86_64 libxml2-devel.x86_64 fontconfig-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("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
# # 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")'
# 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")'
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")'
......@@ -123,10 +135,12 @@ Rscript -e 'devtools::install_github("davidaknowles/leafcutter/leafcutter")'
# # 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")'
# mkdir /usr/bin/leafcutter/
# git clone https://github.com/davidaknowles/leafcutter /usr/bin/leafcutter/
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
......@@ -139,8 +153,9 @@ Rscript -e 'devtools::install_github("davidaknowles/leafcutter/leafcutter")'
# make
# export PATH=${PATH}:/usr/bin/regtools/build/
# %environment
# export PATH=${PATH}:/usr/bin/regtools/build/:/usr/bin/R_3.6.0
%environment
# export PATH=${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"
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment