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Singularity.R4_python368
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Bootstrap: docker
From: continuumio/miniconda3
%environment
export PATH=/opt:/usr/games:/opt/conda/envs/py36/bin:/opt/conda/bin:$PATH
export PYTHONPATH=/opt/conda/envs/py36/lib/python3.6/site-packages/
export LC_ALL=C
%post
#!/bin/bash
eval "$(command conda 'shell.bash' 'hook' 2> /dev/null)"
export PATH=/opt/conda/bin/:$PATH
apt update
yes | apt upgrade
yes | apt-get install build-essential
apt-get install -y --no-install-recommends apt-utils
apt-get install -y gcc-7 g++-7 gfortran-7 libgfortran-7-dev
update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-7 60 --slave /usr/bin/g++ g++ /usr/bin/g++-7
update-alternatives --config gcc
gcc --version
yes | apt-get install wget
yes | apt-get install curl
apt install -y dirmngr --install-recommends
apt install -y software-properties-common
apt install -y apt-transport-https
add-apt-repository 'deb http://deb.debian.org/debian buster-backports main'
yes | apt-get update
yes | apt-get upgrade
apt install -y ca-certificates gnupg2
apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF'
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/debian buster-cran40/'
apt-get update
apt install -y r-base
apt install -y r-base-dev
apt-get update
apt-get install -y libv8-dev
apt-get update
yes | /opt/conda/bin/conda create -n py36 python=3.6.8
cd /opt
CARGO_HOME=/opt/.cargo RUSTUP_HOME=/opt/.cargo bash -c 'curl https://sh.rustup.rs -sSf | sh -s -- -y'
. /opt/.cargo/env
which cargo
rustup default stable
yes | apt-get install git
/opt/conda/bin/conda init bash
eval "$(conda shell.bash hook)"
conda activate py36
yes | apt-get install libncurses5-dev
yes | apt-get install zlib1g-dev
yes | apt-get install libbz2-dev
yes | apt-get install liblzma-dev
# yes | apt-get install cmake
yes | apt-get install zlib1g
yes | apt-get install zlib1g-dev
apt-get install -y pkg-config
apt-get install -y libcurl4-openssl-dev
apt-get install -y graphviz
apt-get install -y graphviz-dev
apt-get install -y libxml2
apt-get install -y libxml2-dev
apt-get install -y bzip2
apt-get install -y libssl-dev
apt-get install -y devscripts
cd /root
wget https://github.com/Kitware/CMake/releases/download/v3.14.4/cmake-3.14.4.tar.gz
tar -xzf cmake-3.14.4.tar.gz
cd cmake-3.14.4
./configure
make
make install
cmake --version
yes | /opt/conda/envs/py36/bin/pip install pysam
/opt/conda/envs/py36/bin/pip install pyvcf
/opt/conda/envs/py36/bin/pip install numpy
/opt/conda/envs/py36/bin/pip install scipy
/opt/conda/envs/py36/bin/pip install pystan==2.17.1.0
/opt/conda/envs/py36/bin/pip install pyfaidx
/opt/conda/envs/py36/bin/pip install scikit-learn
/opt/conda/envs/py36/bin/pip install pandas
/opt/conda/envs/py36/bin/pip install matplotlib==3.2.2
/opt/conda/envs/py36/bin/pip install scikit-image
/opt/conda/envs/py36/bin/pip install numba
/opt/conda/envs/py36/bin/pip install annoy
/opt/conda/envs/py36/bin/pip install umap-learn
/opt/conda/envs/py36/bin/pip install scrublet
/opt/conda/envs/py36/bin/pip install h5py
/opt/conda/envs/py36/bin/pip install snakemake
/opt/conda/envs/py36/bin/pip install Jinja2
/opt/conda/envs/py36/bin/pip install xgboost
cp /opt/conda/lib/libstdc++.so.6.0.26 /usr/lib/x86_64-linux-gnu/
mv /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.bkp
ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.26 /usr/lib/x86_64-linux-gnu/libstdc++.so.6
R --slave -e 'install.packages("V8", repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("rversions", repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("devtools", repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("tidyverse", repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("data.table", repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("Seurat", repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("remotes", repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("xgboost", repos = "http://cran.us.r-project.org")'
R --slave -e 'devtools::install_github(repo="knausb/vcfR")'
R --slave -e 'devtools::install_github("kostkalab/scds", ref="master")'
R --slave -e 'install.packages("BiocManager")'
R --slave -e 'BiocManager::install("clusterProfiler")'
R --slave -e 'install.packages("MCL", repos = "http://cran.us.r-project.org")'
R --slave -e 'BiocManager::install("mygene")'
R --slave -e 'install.packages("R.utils", repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("foreach", repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("doParallel", repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("locfit", repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("ggplot2", repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("ggpubr", repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("ggnewscale", repos = "http://cran.us.r-project.org")'
R --slave -e 'install.packages("RColorBrewer", repos = "http://cran.us.r-project.org")'
R --slave -e 'devtools::install_github(repo="knausb/vcfR")'
R --slave -e 'install.packages("lsa", repos = "http://cran.us.r-project.org")'
R --slave -e 'BiocManager::install("ComplexHeatmap")'