Software library for recoding genomes used in Ostrov et al. (2016). Design, synthesis, and testing toward a 57-codon genome. Science, 353(6301).
Please contact us if you're interested in using this software for your own recoding projects: Gleb Kuznetsov ([email protected])
The software was developed and tested using python 2.7.
The required python libraries are listed in requirements.txt. We recommend
using virtualenv to create a
sandboxed environment.
virtualenv venv
source venv/bin/activate .
pip install -r requirements.txt
-
Download and install from here:
http://homepages.rpi.edu/~zukerm/download/UNAFold_download.html
If using Linux, you probably want to download the RPM and use these instructions: https://overlappingminds.com/sh/thoughts/0aa6d79e-fb8b-4f84-b287-f8e4494eac49
cd src/
git clone [email protected]:hsalis/Ribosome-Binding-Site-Calculator-v1.0.git rbs_calc
cd rbs_calc/
touch __init__.py
-
Download here http://www.nupack.org/. Our software expects Nupack to be located at /opt/nupack/. So either install it there, or update
src/refactor_config.py. -
Copy the files in bin/ to /usr/local/bin
-
Test that
hybrid-ss-mincan be run from the shell. Test the following command in a new terminal:hybrid-ss-min -h
If using virtualenv, be sure the correct python environment is activated.
cd src/
./run_tests.sh
The main entry point to the code is src/main.py. After setting up the proper Python environment, you should be able to simply run:
cd src/
python main.py
Results are written to src/output.
Copyright (C) 2016 The President and Fellows of Harvard College
The Genome Recoder software is available under an internal non-commercial research and academic use license. Questions about this software or the licensing thereof can be addressed to Office of Technology Development, Harvard University, email: [email protected].
See the LICENSE file.