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Metagenome program installation

Authored by Jackson Sorensen
EDAMAME-2015 wiki


EDAMAME tutorials have a CC-BY license. Share, adapt, and attribute please!


##Overarching Goal

  • This tutorial will contribute towards an understanding of microbial metagenome analysis and developing computing literacy.

##Learning Objectives

  • Install axillary software on an Amazon EC2 instance
  • Recognize that there is not one tool for an entire metagenome analysis

For this course, we will be using a set of independently developed programs for our metagenome analysis. While some of the programs are already installed on your EC2 instance there are a few remaining that we will download and install together as a class. These include the FastX toolkit and one of its dependencies Libgtextutils, as well as Khmer. You will need to be running an m3.large EC2 instance from the AMI EDAMAME-2015 with 100GB of storage.

####Downloading, Unpacking, and Installing Libgtextutils and FastX: In order to install FastX and libgtextutils we will do three basic steps. First we will download a compressed version of the programs using wget. Then we will unzip those folders using tar and finally we will install configure and install the programs. The code for install these two programs are listed below.

#####For libgtextutils

wget https://github.com/agordon/libgtextutils/releases/download/0.7/libgtextutils-0.7.tar.gz
tar -zxvf libgtextutils-0.7.tar.gz
cd libgtextutils-0.7
./configure
make
sudo make install

#####For FastX:

wget https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2
tar -xjf fastx_toolkit-0.0.14.tar.bz2
cd fastx_toolkit-0.0.14
./configure
make
sudo make install

####Installing Khmer: While installing khmer, we will do things slightly differently. We will start by moving into the directory /usr/local/share/ and the use the command git clone to download the khmer programs. We'll then change into the new directory using cd and then install khmer.

cd /usr/local/share/
sudo git clone https://github.com/ged-lab/khmer.git
cd khmer
sudo git checkout protocols-v0.8.3
sudo make

echo 'export PYTHONPATH=/usr/local/share/khmer:$PYTHONPATH' >> ~/.bashrc
source ~/.bashrc

####Installing screed:

sudo pip install screed
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