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.