traitar is available for Linux via the python packaging index. We tested the software under Ubuntu 14.04 LTS (trusty). We didn't test older versions but these might work as well. Prior to installation with pip make sure the following packages are installed by running
sudo apt-get install python-scipy python-matplotlib python-pip python-pandas
and optionally
sudo apt-get install python-virtualenv
These package might not be available for your Linux distribution. Please let us know, if you have troubles installing this software, so that we can assist you with the installation.
Once finished we strongly encourage you to install traitar with pip rather than by manually cloning the repository. Install locally by
pip install traitar-<version>.tar.gz --user
You need to add the following line to your ~/.bashrc to adjust the PATH variable so that the bash finds the executables needed for running traitar.
PATH=$PATH:~/.local/bin/
You may need to run source ~/.bashrc once in your current session.
You can also install globally with
sudo pip install traitar-<version>.tar.gz
You may want to use virtualenv to create a clean environment for traitar i.e. run
virtualenv <environment_name> --system-site-packages
source <environment_path>/bin/activate
pip install -U traitar-<version>.tar.gz
PATH=$PATH:<environment_path>/bin/
source ~/.bashrc
traitar further needs prodigal and hmmsearch available on the command line. For parallel execution it further requires GNU parallel. All three are available as preconfigured package for many Linux installation e.g. for Debian / Ubuntu. For Ubuntu 14.04 it is available via the trusty-backports.
#include trusty backports source in the sources.list
"sudo deb http://archive.ubuntu.com/ubuntu trusty-backports main restricted universe multiverse ">> /etc/apt/sources.list
#update sources
apt-get install update
#install packages
sudo apt-get install parallel prodigal hmmer
traitar -h will provide help regarding the different options of traitar.
traitar requires the Pfam 27.0 HMM models. These are not distributed with this package but need to be downloaded
traitar pfam <path to download folder>
will download and extract the Pfam models to the specified folder. The download can take a while depending on you internet connection. The Pfam models are extracted automatically to the same folder. This can slow down some machines. You may also download and extract the Pfam models manually from ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam27.0/Pfam-A.hmm.gz and run
traitar pfam --local <path to Pfam folder>
to let traitar know where.