Setup your AWS instance

This lesson will show you how to set up you AWS instance for general use. Most lessons will use a similar process, though the specific software installed may vary.

In General, there are a few differnet ways to install software. Installing from source, installing from apt-get, installing from Brew, pip, etc. You’ll get to know each of these packages over the course of the next two weeks.

Launch a c4.2xl instance

Update System Software This command will check for updates, and install them. apt-get is like the OSX App store, for those of you with Macs.

sudo apt-get update && sudo apt-get -y upgrade

Install Basic System Software This command will install various software on your AWS instance.

sudo apt-get -y install build-essential cmake sparsehash valgrind libibnetdisc-dev gsl-bin \
    libgsl0-dev libgsl0ldbl  subversion tmux git curl parallel gcc make g++ zlib1g-dev \
    libncurses5-dev  python-dev unzip dh-autoreconf default-jre python-pip \
    mcl libhdf5-dev r-base pkg-config libpng12-dev libfreetype6-dev libsm6 \
    libxrender1 libfontconfig1 liburi-escape-xs-perl liburi-perl

Install Ruby Ruby is a computer language like Python or Perl.

gpg --import key.asc
\curl -sSL | bash -s stable --ruby
source /home/ubuntu/.rvm/scripts/rvm

Install Brew Brew is a piece of software the serves as a ‘package manager’. It makes installing software easy! You can use it for lots of things, but not everything. Knowing it’s limitations will come with time.

ruby -e "$(curl -fsSL"

# press return

echo 'export PATH="/home/ubuntu/.linuxbrew/bin:$PATH"' >>~/.profile
echo 'export MANPATH="/home/ubuntu/.linuxbrew/share/man:$MANPATH"' >>~/.profile
echo 'export INFOPATH="/home/ubuntu/.linuxbrew/share/info:$INFOPATH"' >>~/.profile
source ~/.profile

Install Python Packages This will take some time...

pip install --user biopython

Install BLAST

curl -LO
tar -zxf ncbi-blast-2.4.0+-x64-linux.tar.gz

Install Bioinformatics Packages via Brew These are the packages that we will use to do real work!!! YAY!!!

brew tap homebrew/science
brew install hmmer
brew install augustus
brew install emboss
brew install busco --without-blast

How to tell if something is installed

which blastp
which busco

** Most of the lessons** will start by installing these types of software. Practice makes perfect. Try terminating your instance, restarting, and reinstalling...

TERMINATE your instance

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