“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.
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 \ 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/v1/files/BUSCO_v1.22.tar.gz tar -xvzf BUSCO_v1.22.tar.gz chmod +x BUSCO_v1.22/*.py export PATH=$HOME/BUSCO_v1.22:$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' >> $HOME/.bashrc echo 'export PATH=$HOME/BUSCO_v1.22:$PATH' >> $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 if you don’t already have a recent versions installed; the ones available in the Ubuntu 14.04 archives are just too old.
If you want the latest features (and bugs), you can install dammit from github:
pip install git+https://github.com/camillescott/dammit.git
To check for dependencies, run:
To check for databases, run:
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.
- On some systems, installation of the ConfigParser package can get borked, which will cause and exception to be thrown. This can be fixed by following the directions at issue #33: https://github.com/camillescott/dammit/issues/33.
- 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 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.
- dammit 0.3 does not support BUSCO v2. dammit 1.0 is building 2.0 support in.
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.