dammit 0.2.9

dammit!

“I love writing BLAST parsers!” – no one, ever

dammit is a simple de novo transcriptome annotator. It was born out of the observation that: annotation is mundane and annoying; all the individual pieces of the process exist already; and, the existing solutions are overly complicated or rely on crappy non-free software.

Science shouldn’t suck for the sake of sucking, so dammit attempts to make this sucky part of the process suck a little less.

Installation

Complete instructions with explanations and more platform options are in the documentation website. For the impatient, here’s a stripped down version. These instructions assume you’re on a clean Ubuntu 14.04 install. dammit will run on OSX too, though some of the dependencies will need to be installed manually and are not included here.

First get packages from the Ubuntu archives:

sudo apt-get update
sudo apt-get install python-pip python-dev python-numpy git ruby hmmer unzip \
    infernal ncbi-blast+ liburi-escape-xs-perl emboss liburi-perl \
    python-sklearn build-essential libsm6 libxrender1 libfontconfig1 \
    parallel
sudo gem install crb-blast

Install some packages manually:

cd
curl -LO 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=$HOME/TransDecoder-2.0.1:$PATH

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

cd
curl -LO 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=$HOME/BUSCO_v1.1b1:$PATH
cd

To add these to your environment permanently:

echo 'export PATH=$PATH:$HOME/TransDecoder-2.0.1' >> $HOME/.bashrc
echo 'export PATH=$PATH:$HOME/last-658/src' >> $HOME/.bashrc
echo 'export PATH=$PATH:$HOME/BUSCO_v1.1b1' >> $HOME/.bashrc

Now, install dammit:

sudo pip install -U setuptools
sudo pip install dammit

This will spend a bit of time compiling and installing pandas and scikit-learn if you don’t already have a recent versions installed; the ones available in the Ubuntu 14.04 archives are just too old.

Usage

To check for dependencies, run:

dammit dependencies

To check for databases, run:

dammit databases

and to download and install them, run:

dammit databases --install

To annotate your transcriptome, the most basic usage is:

dammit annotate <transcriptome_fasta>

These are extremely basic examples; for a much more detailed description, take a look at the relevant page in the documentation. The documentation describes how to customization the database installation location and utilize existing databases.

Known Issues

• Currently, the –full option is a no-op; it will be reactivated in a future release.

• There can be errors resuming runs which were interrupted on the BUSCO stage. If the task fails on resume, delete the BUSCO results folder within your dammit results folder, which will have a name of the form run_<name>.busco_results.

• The GFF3 coordinates for the hmmscan/Pfam-A results are currently being reported incorrectly – they are relative to the predicted ORFs, and should be relative to the transcripts. This is a top-priority issue.

• The dependencies subcommand doesn’t search for all subdependencies; for example, BUSCO relies on EMBOSS, which is not searched for. Although the installation instructions cover these dependencies, users who cough don’t read the directions cough might be confused that a dependency is marked as installed but still doesn’t work.

Acknowledgements

I’ve received input and advice from a many sources, including but probably not limited to: C Titus Brown, Matt MacManes, Chris Hamm, Michael Crusoe, Russell Neches, Luiz Irber, Lisa Cohen, Sherine Awad, and Tamer Mansour.

CS is funded by the National Human Genome Research Institute of the National Institutes of Health under Award Number R01HG007513 through May 2016, and also receives support from the Gordon and Betty Moore Foundation under Award number GBMF4551.