Emotif Alpha: an optimized motif discovery pipeline¶

General principles¶

A typical Emotif Alpha command looks like this:

Emotif_Alpha -jid myJobID -confFile motif.config

Installation¶

Step 0: Anaconda python 2.7

Currently, Emotif Alpha is only working in python2.7. The next release will be updated to python 3.

Step 1: Install GimmeMotifs

GimmeMotifs GimmeMotifs is a collection of motif discovery tools. The most straightforward way to install GimmeMotifs (https://github.com/simonvh/gimmemotifs ) is:

conda install -c bioconda gimmemotifs

Step 2: Install DME

In the next release, I will include these commands inside setup.py.

git clone https://github.com/smithlabcode/dme

cd dme

https://github.com/smithlabcode/smithlab_cpp.git

make

./dme2 (you should be able to see the help message)

If you see an error when compling the source code, one possible reason is that you don’t have the latest gcc version. The one I’m using is gcc/6.3.0.

Step 2: Install DECOD

wget http://www.sb.cs.cmu.edu/DECOD/download/DECOD-V1.01-20111024.zip

unzip DECOD-V1.01-20111024.zip

java -jar DECOD-20111024.jar -nogui   (you should be able to see the help message)

# add to bashrc

alias decod='java -jar /home/yli11/Programs/jar_tools/DECOD-20111024.jar -nogui'

Step 3: Install scikit-learn and BioPython

conda install -c anaconda scikit-learn

conda install -c conda-forge biopython

Step 4: Install R ggplot2

R

install.packages("devtools")

devtools::install_github("hadley/ggplot2")

Step 5: Install MEME suite

ref: http://meme-suite.org/doc/install.html?man_type=web

You will use meme, meme2images, and fimo here.

Step 4: Install Emotif Alpha

sudo python setup.py install

Usage¶

TO OBTAIN A COPY OF SAMPLE CONFIGURATION FILE

Emotif_alpha -copy any_name.conf

TO RUN THE TEST DATASET

Emotif_alpha -jid some_name -confFile any_name.conf

The pipeline configuration file¶

FAQ¶

wrong GimmeMotifs command? Depends on the GimmeMotifs version, the command in the motif_discovery.py might not be correct. It is in line 364.