This is a pipeline for finding motifs in fasta files.
It can be run from the command line as follows:

usage: orange_pipeline_refine.py [-h] [-w W] [--nmotifs NMOTIFS] [--iter ITER] [-c C]
[-s S] [-d] [-ff] [-v V]
positive_seq negative_seq

positional arguments:
positive_seq the fasta file for the positive sequences
negative_seq the fasta file for the negative sequences

optional arguments:
-h, --help show this help message and exit
-w W motif width
--nmotifs NMOTIFS max number of distinct motifs to look for
--iter ITER max number of iterations (for DECOD tool)
-c C config filename
-s S statfile directory
-d turn debug mode on
-ff force (re)filtering
-v V number of results to include in visual output

This pipeline makes use of 6 publicly available 3rd party tools:
DECOD
MEME
CMF
BioProspector
Weeder
XXmotif

This distribution includes the source for all of these tools, as well as 64-bit and 32-bit executables compiled on linux. If you are using Windows or MacOS, you might need to recompile some of the tools on your platform and replace the relevant executables.
All of these sources were downloaded from their respective websites and are unaltered with the exception of 2 small file path changes in Weeder to account for our pipeline not providing files the way weeded expected.

Requirements:
Java 1.8
Python 2.7 SciPy 0.19.0 NumPy 1.12.1 MatPlotLib 1.2.0
perl 5.16.3
Chostscript 9.07