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Installation
The following instructions describe how to install the msbwt package. This will install both the msbwt command line tool and the libraries necessary to access the Python API.
The easiest way to install msbwt is to use an automated installer to compile the files and set up all executables to be used from the command line. To install universally on a Mac or Linux machine:
easy_install msbwt
OR:
pip install msbwt
If for some reason, you do not have admin privileges on your machine, then using the "--user" option will perform a local installation of msbwt:
pip install --user msbwt
Run the following command to verify the msbwt command line interface is accessible:
msbwt -h
The releases of msbwt can be downloaded at https://github.com/holtjma/msbwt/releases. For version 0.2.9, use the following commands to download and install msbwt:
wget https://github.com/holtjma/msbwt/archive/0.2.9.tar.gz
tar -xzvf 0.2.9.tar.gz
cd msbwt-0.2.9
python setup.py install
The above will install the msbwt universally. To do a local (user) install, replace the last command with:
python setup.py install --user
Holt, J., & McMillan, L. (2014). Merging of multi-string BWTs with applications. Bioinformatics, btu584.
Holt, J., & McMillan, L. (2014, September). Constructing burrows-wheeler transforms of large string collections via merging. In Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 464-471). ACM.
James Holt - [email protected]