Metagenome program installation
Authored by Jackson Sorensen
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- This tutorial will contribute towards an understanding of microbial metagenome analysis and developing computing literacy.
- 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.
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
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
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
sudo pip install screed