“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 are at the documentation website. For the impatient, here’s a stripped down version.
These instructions assume you’re on Ubuntu 14.04. dammit will run on OSX too, though some of the dependencies will need to be installed manually.
Anaconda is the recommended python distribution, or at the very least, virtualenv to manage your python packages. Once you have a working python environment, proceed as follows:
pip install -U setuptools pip install dammit
Get packages from the Ubuntu PPAs:
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 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=$PATH:$HOME/TransDecoder-2.0.1 cd curl -LO http://last.cbrc.jp/last-658.zip unzip last-658.zip cd last-658 make export PATH=$PATH:$HOME/last-658/src 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=$PATH:$HOME/BUSCO_v1.1b1 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
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.
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