New VM setup script for Ubuntu 22.04

new-vm-setup.sh

################################################################################
# GCP/AWS setup script for general bioinformatics
# Base image: Ubuntu 22.04 LTS x86/64
################################################################################

# Make a directory in which to build stuff
sudo mkdir -p ${HOME}/build && sudo chmod 777 ${HOME}/build && cd ${HOME}/build

# Install system libs
sudo apt-get update
sudo apt-get install -y \
    apt-transport-https \
    build-essential \
    ca-certificates \
    cloud-guest-utils \
    curl \
    default-jre \
    f2c \
    gdebi-core \
    gnupg \
    libbz2-dev \
    libcurl4-openssl-dev \
    libffi-dev \
    libfontconfig1-dev \
    libfribidi-dev \
    libgsl0-dev \
    libgtextutils-dev \
    libharfbuzz-dev \
    libicu-dev \
    liblzma-dev \
    libncurses5-dev \
    libncursesw5-dev \
    libpcre3 \
    libpcre3-dev \
    libperl-dev \
    libreadline-dev \
    libssl-dev \
    libtiff-dev \
    libxml2-dev \
    locales \
    ncftp \
    pandoc \
    parallel \
    pkg-config \
    readline-doc \
    sudo \
    tcl \
    tk \
    tk-dev \
    tk-table \
    tmux \
    tzdata \
    unzip \
    vim \
    && sleep 1

# Optionally set the time zone (to the best time zone -- use Etc/UTC if you're not sure)
sudo timedatectl set-timezone America/New_York

# Set locale
sudo locale-gen en_US.UTF-8

# Install latest version of R
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo gpg --dearmor -o /usr/share/keyrings/r-project.gpg
echo "deb [signed-by=/usr/share/keyrings/r-project.gpg] https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" | sudo tee -a /etc/apt/sources.list.d/r-project.list
sudo apt update
sudo apt install -y r-base
echo 'options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/latest"))' | sudo tee -a /usr/lib/R/etc/Rprofile.site

# # Install a specific version of R
# export R_VERSION="4.2.3"
# sudo curl -O https://cdn.rstudio.com/r/ubuntu-2204/pkgs/r-${R_VERSION}_1_amd64.deb
# sudo gdebi -n r-${R_VERSION}_1_amd64.deb
# sudo ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R
# sudo ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript
# echo 'options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/latest"))' | sudo tee -a /opt/R/4.2.3/lib/R/etc/Rprofile.site

# Install RStudio server
cd ${HOME}/build
wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2024.04.1-748-amd64.deb
sudo gdebi --non-interactive rstudio-server-2024.04.1-748-amd64.deb

# Install gcloud and gsutils
# https://cloud.google.com/sdk/docs/install#deb
curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | sudo gpg --dearmor -o /usr/share/keyrings/cloud.google.gpg
echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] https://packages.cloud.google.com/apt cloud-sdk main" | sudo tee -a /etc/apt/sources.list.d/google-cloud-sdk.list
sudo apt-get update && sudo apt-get install google-cloud-cli
# gcloud auth login

# GCSfuse
export GCSFUSE_REPO=gcsfuse-`lsb_release -c -s`
echo "deb [signed-by=/usr/share/keyrings/cloud.google.asc] https://packages.cloud.google.com/apt $GCSFUSE_REPO main" | sudo tee /etc/apt/sources.list.d/gcsfuse.list
curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | sudo tee /usr/share/keyrings/cloud.google.asc
sudo apt-get update
sudo apt-get install gcsfuse

# Nextflow
cd ${HOME}/build
# Get the latest build
wget -qO- https://get.nextflow.io | bash
sudo mv nextflow /usr/local/bin
sudo chmod 755 /usr/local/bin/nextflow

# Docker
sudo install -m 0755 -d /etc/apt/keyrings
sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
sudo chmod a+r /etc/apt/keyrings/docker.asc
echo \
  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \
  $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | \
  sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt-get update
sudo apt-get install -y docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
sudo groupadd docker
sudo usermod -aG docker $USER

################################################################################
# Domain specific tools
################################################################################

# Seqkit
# https://github.com/shenwei356/seqkit/
cd ${HOME}/build
VERSION_SEQKIT="2.8.1"
wget https://github.com/shenwei356/seqkit/releases/download/v${VERSION_SEQKIT}/seqkit_linux_amd64.tar.gz
tar xzf seqkit_linux_amd64.tar.gz
sudo mv seqkit /usr/local/bin

# fastp
# https://github.com/OpenGene/fastp
cd ${HOME}/build
wget http://opengene.org/fastp/fastp
chmod a+x ./fastp
sudo mv fastp /usr/local/bin

# Seqtk
# https://github.com/lh3/seqtk
cd ${HOME}/build
VERSION_SEQTK="1.4"
wget -q https://github.com/lh3/seqtk/archive/refs/tags/v${VERSION_SEQTK}.tar.gz
tar xzf v${VERSION_SEQTK}.tar.gz
cd seqtk-${VERSION_SEQTK}
make && sudo make install

# htslib, samtools, bcftools
VERSION_SAMTOOLS="1.20"
## htslib
cd ${HOME}/build
wget -q https://github.com/samtools/htslib/releases/download/${VERSION_SAMTOOLS}/htslib-${VERSION_SAMTOOLS}.tar.bz2
tar xjf htslib-${VERSION_SAMTOOLS}.tar.bz2
cd htslib-${VERSION_SAMTOOLS}
./configure && make -j4 && sudo make install
## bcftools
cd ${HOME}/build
wget -q https://github.com/samtools/bcftools/releases/download/${VERSION_SAMTOOLS}/bcftools-${VERSION_SAMTOOLS}.tar.bz2
tar xjf bcftools-${VERSION_SAMTOOLS}.tar.bz2
cd bcftools-${VERSION_SAMTOOLS}
./configure && make -j4 && sudo make install
# samtools
cd ${HOME}/build
wget -q https://github.com/samtools/samtools/releases/download/${VERSION_SAMTOOLS}/samtools-${VERSION_SAMTOOLS}.tar.bz2
tar xjf samtools-${VERSION_SAMTOOLS}.tar.bz2
cd samtools-${VERSION_SAMTOOLS}
./configure && make -j4 && sudo make install

# bedtools
# https://github.com/arq5x/bedtools2
cd ${HOME}/build
VERSION_BEDTOOLS="2.31.1"
wget https://github.com/arq5x/bedtools2/releases/download/v${VERSION_BEDTOOLS}/bedtools-${VERSION_BEDTOOLS}.tar.gz
tar xzf bedtools-${VERSION_BEDTOOLS}.tar.gz
cd bedtools2
make -j4 && sudo make install

# bwa
# https://github.com/lh3/bwa/
VERSION_BWA="0.7.18"
cd ${HOME}/build
wget -q https://github.com/lh3/bwa/archive/refs/tags/v${VERSION_BWA}.tar.gz
tar xzf v${VERSION_BWA}.tar.gz
cd ${HOME}/build/bwa-${VERSION_BWA}
# make CC='gcc -fcommon'
make
sudo mv bwa /usr/local/bin/
sudo mv bwa.1 /usr/local/share/man/man1

# minimap2
# https://github.com/lh3/minimap2/
cd ${HOME}/build
VERSION_MINIMAP2="2.28"
wget -q https://github.com/lh3/minimap2/releases/download/v${VERSION_MINIMAP2}/minimap2-${VERSION_MINIMAP2}.tar.bz2
tar xjf minimap2-${VERSION_MINIMAP2}.tar.bz2
cd minimap2-${VERSION_MINIMAP2}
make
sudo mv minimap2 /usr/local/bin/
sudo mv minimap2.1 /usr/local/share/man/man1

# bowtie2
# https://github.com/BenLangmead/bowtie2
cd ${HOME}/build
VERSION_BOWTIE2="2.5.3"
wget https://github.com/BenLangmead/bowtie2/releases/download/v${VERSION_BOWTIE2}/bowtie2-${VERSION_BOWTIE2}-linux-x86_64.zip
unzip bowtie2-${VERSION_BOWTIE2}-linux-x86_64.zip
sudo mv bowtie2-${VERSION_BOWTIE2}-linux-x86_64/bowtie2* /usr/local/bin

# Clean up the build dir
cd && sudo rm -rf ${HOME}/build


################################################################################
# Interactive installs and setup
################################################################################

# Mamba
wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash Miniforge3-Linux-x86_64.sh

# Authorize gcloud
gcloud auth login
gcloud config set compute/region us-central1
gcloud config set project your-project-id

# After adding an ssh key: Get dotfiles, and replace the Rprofile repos
cd ${HOME}
git clone [email protected]:stephenturner/dotfiles.git
cd dotfiles
./install.sh

# Optionally relocate docker data-root to a different disk
# Assumes new disk is mounted at /data
NEWDOCKERDIR=/data/docker
sudo systemctl stop docker
sudo systemctl stop docker.socket
sudo systemctl stop containerd
sudo mkdir -p $NEWDOCKERDIR
sudo mv /var/lib/docker $NEWDOCKERDIR
sudo vim /etc/docker/daemon.json
## Add the following (replace the directory with the correct path):
# {
#   "data-root": "/data/docker"
# }
sudo systemctl start docker
docker info -f '{{ .DockerRootDir}}'

# Set up R profile to use RSPM
echo 'options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/latest"))' >> ~/.Rprofile