prepare_2018

Configuration on Ubuntu 14.04.5LTS

Software and Hardware versions

• Ubuntu: 14.04.5
• Universal USB Installer: 1.9.5.9
• Lenovo PC: V3000
• USB-Disk: Sandisk

Install Ubuntu

• Use Universal USB Installer 1.9.5.9 to build Ubuntu 14.04.5LTS.
  • See more from https://universal-usb-installer.en.softonic.com/  

Steps on Ubuntu

cd

• Install Ubuntu packages

bash prepare_2018/1-apt.sh | tee log-1-apt.txt

• Build unity

bash prepare_2018/2-unity.sh

• Install Linuxbrew

echo '==> Install Linuxbrew'
sh -c "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install.sh)"

test -d ~/.linuxbrew && PATH="$HOME/.linuxbrew/bin:$HOME/.linuxbrew/sbin:$PATH"
test -d /home/linuxbrew/.linuxbrew && PATH="/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:$PATH"
test -r ~/.profile && echo "export PATH='$(brew --prefix)/bin:$(brew --prefix)/sbin'":'"$PATH"' >>~/.profile
echo "export PATH='$(brew --prefix)/bin:$(brew --prefix)/sbin'":'"$PATH"' >>~/.profile

if grep -q -i linuxbrew $HOME/.bashrc; then
    echo "==> .bashrc already contains linuxbrew"
else
    echo "==> Update .bashrc"
    echo >> $HOME/.bashrc
    echo '# Linuxbrew' >> $HOME/.bashrc
    echo "export PATH='$(brew --prefix)/bin:$(brew --prefix)/sbin'":'"$PATH"' >> $HOME/.bashrc
    echo "export MANPATH='$(brew --prefix)/share/man'":'"$MANPATH"' >> $HOME/.bashrc
    echo "export INFOPATH='$(brew --prefix)/share/info'":'"$INFOPATH"' >> $HOME/.bashrc
    echo "export HOMEBREW_NO_ANALYTICS=1" >> $HOME/.bashrc
    echo >> $HOME/.bashrc
fi

• Install CLI apps via Homebrew/Linuxbrew

bash prepare_2018/3-brew.sh | tee log-3-brew.txt

• Install Perl Python and R

bash prepare_2018/perl/install.sh | tee log-perl.txt
bash prepare_2018/python/install.sh | tee log-python.txt
bash prepare_2018/r/install.sh | tee log-r.txt

• Install bioinformatics apps via Homebrew science and homebrew-tap. Install Trinity manually.

bash prepare_2018/4-genomics.sh | tee log-4-genomics.txt

• Do other clones and downloads

bash prepare_2018/5-clone.sh | tee log-5-clone.txt
bash prepare_2018/6-download.sh | tee log-6-download.txt

• Install other bioinfomatics softwares

bash prepare_2018/7-bioinfo.sh | tee log-7-bioinfo.txt

• Install GATK4. GATK4 contains a copy of the Picard toolkit.

aria2c -x 4 https://github.com/broadinstitute/gatk/releases/download/4.1.1.0/gatk-4.1.1.0.zip
## It might take many times because the connection is very poor. Or you can download it by a Windows PC.
unzip gatk-4.1.1.0.zip
echo >> $HOME/.bashrc
echo "# GATK4" >> $HOME/.bashrc
echo "export PATH='$(HOME)/gatk-4.1.1.0'":'"$PATH"' >> $HOME/.bashrc
echo >> $HOME/.bashrc
source .bashrc

• Install MySQL and Ensembl

bash prepare_2018/8-mysql.sh | tee log-8-mysql.txt
bash prepare_2018/9-ensembl.sh | tee log-9-ensembl.txt       # Optional, needed by alignDB

Building steps is completed.