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Installation

Installation

dammit itself is quite easy to install. Just run:

pip install dammit

If you get an error about using an outdated version of setuptools, you'll need to update that first:

pip install -U setuptools

Generally I recommend trying to maintain some sort of environment structure. This can be done with virtualenv or anaconda environments.

However, unless you have all the dependencies installed already, it won't work yet! You can check if they are by running:

dammit dependencies

Which will report which ones are missing.

Dependencies

Unfortunately, annotation necessarily relies on many software packages. I have worked hard to make dammit rely only on software which is accessible and likely to continue to be so. Most of the dependencies are available in either Ubuntu PPAs or PyPI, and if not, are trivial to install manually. If the goal is to make annotation suck less, then installing the necessary software should suck less too.

Most of this guide will assume you're on a Ubuntu system. However, the dependencies should all run on any flavor of GNU/Linux and on OSX.

First, let's get packages from the Ubuntu PPAs:

sudo apt-get update
sudo apt-get install python-pip python-dev python-numpy git ruby hmmer \
    infernal ncbi-blast+ liburi-escape-xs-perl emboss liburi-perl

If you're on Ubuntu 15.10, you can also install TransDecoder and LAST through aptitude:

sudo apt-get install transdecoder last-align

Otherwise, you'll need to install them manually. To install TransDecoder in your home directory, execute these commands in your terminal:

cd
curl -O https://github.com/TransDecoder/TransDecoder/archive/2.0.1.tar.gz
tar -xvzf 2.0.1.tar.gz
cd TransDecoder-2.0.1; make
export PATH=$PATH:$HOME/TransDecoder-2.0.1

To get LAST:

cd
curl -O http://last.cbrc.jp/last-658.zip
unzip last-658.zip
cd last-658
make
export PATH=$PATH:$HOME/last-658

The above commands will only install them for the current session; to keep it installed, append the exports to your bash profile:

echo 'export PATH=$PATH:$HOME/TransDecoder-2.0.1' >> $HOME/.bashrc
echo 'export PATH=$PATH:$HOME/last-658' >> $HOME/.bashrc

Next, we need to install Conditional Reciprocal Best-hits Blast (CRBB). The algorithm is described in Aubry et al., and is implemented in ruby. Assuming you have ruby, it can be installed with:

sudo gem install crb-blast

dammit also runs BUSCO to assess completeness. To install it, run the following commands:

cd
curl -O http://busco.ezlab.org/files/BUSCO_v1.1b1.tar.gz
tar -xvzf BUSCO_v1.1b1.tar.gz
chmod +x BUSCO_v1.1b1/*.py
export PATH=$PATH:$HOME/BUSCO_v1.1b1

...and once again, to install it permanently:

echo 'export PATH=$PATH:$HOME/BUSCO_v1.1b1' >> $HOME/.bashrc

When you're done, run the check again to make sure everything was installed correctly:

dammit dependencies