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.
cd
wget https://keybase.io/mpapis/key.asc
gpg --import key.asc
\curl -sSL https://get.rvm.io | 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 "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install)"
# press return
echo 'export PATH="/home/ubuntu/.linuxbrew/bin:$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 ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.4.0+-x64-linux.tar.gz
tar -zxf ncbi-blast-2.4.0+-x64-linux.tar.gz
PATH=$PATH:$HOME/ncbi-blast-2.4.0+/bin
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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