pufengdu / ultrapse

A universal and extensible software platform for biological sequence representations

UltraPse

An extensible software platform for biological sequence representations

Installation

Source code in this repositiory is for Ubuntu Linux platform. We have tested these codes on Ubuntu 14.04.5 LTS. There is no guarantee that these codes can be compiled and executed on other platforms without modifications.

These codes depend on the lua-devel version 5.3. It has been proven that lower version will NOT work. Please go to http://www.lua.org/download.html. Download version 5.3 lua environment and configure that on your machine.

After your lua environment is ready, find out the location of your lua.hpp and liblua.a. They usually reside in positions like xxxx/lua-5.3.4/install/include and xxxx/lua-5.3.4/install/lib, where xxxx is usually the directory you unpack your lua source codes.

Suppose the xxxx equals to ~/bin. You should then EDIT the following two lines of the Makefile of UltraPse.

EXT_HEADER=~/bin/lua-5.3.4/install/include

EXT_LIB=~/bin/lua-5.3.4/install/lib

After saving the Makefile, just type make. You will get UltraPse compiled. The upse is the executable of UltraPse software. To test your compilation, just type ./upse --help or ./upse -q prop -n stdprot

To do more test, please first make modules. This will make the one-hot mode BSO.

You can type make test to test UltraPse with TDFs.

You can type make test_mod to test UltraPse with BSOs.

For Microsoft Windows platform, just download the Win-x86_64.zip package from Release/Win-x86_64. Unpack it to your favoured location and use command line environment to use the executable. The documents, plugins, and test datasets are included.

For Microsoft Windows platform, you can use the upse-test.cmd to have a quick view.

If you got any difficulties, just send emails to [email protected] to complain. We will try out best to fix it asap.

Citation

Please cite the following paper if you find UltraPse useful in your work:

[1] Du, Pu-Feng; Zhao, Wei; Miao, Yang-Yang; Wei, Le-Yi; Wang, Likun. 2017. "UltraPse: A Universal and Extensible Software Platform for Representing Biological Sequences." Int. J. Mol. Sci. 18, no. 11: 2400. http://dx.doi.org/10.3390/ijms18112400