gimmemotifs 0.11.1

GimmeMotifs is a motif prediction pipeline.

Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments.

See full GimmeMotifs documentation for detailed installation instructions and usage examples.

For documentation on the development version see here.

Easy installation

The most straightforward way to install GimmeMotifs is via conda using the bioconda channel. If you have not used bioconda yet, first set up the necessary channels (in this order):

$ conda config --add channels r
$ conda config --add channels defaults
$ conda config --add channels conda-forge
$ conda config --add channels bioconda

Normally, you would be able to install GimmeMotifs with one command:

$ conda create -n gimme gimmemotifs

However, due to an issue with the bioconda build system, I can’t release the current stable version on bioconda. Until that is fixed, you can install it as follows:

# Create an environment called gimme with all dependencies
$ conda create -n gimme python=3 pip future numpy scipy matplotlib=2 \
statsmodels scikit-learn seaborn jinja2 bedtools pybedtools \
ucsc-genepredtobed lightning xgboost r-robustrankaggreg pillow pyyaml \
diskcache six ucsc-bigbedtobed xdg xxhash readline ghostscript homer \
gadem trawler weeder xxmotif

# Activate the environment
$ source activate gimme

# Install gimmemotifs
$ pip install https://github.com/simonvh/gimmemotifs/releases/download/0.11.1/gimmemotifs-0.11.1.tar.gz

Python 3 is the preferred version, however, GimmeMotifs also supports Python 2. Don’t forget to activate the environment with source activate gimme whenever you want to use GimmeMotifs.

Quick start

Download a genome

Create a directory to store genome files.

$ mkdir $HOME/genomes/

To download and index a genome (all UCSC-supported genomes):

$ gimme genome $HOME/genomes/ hg38

Alternatively, you can index a genome directory with chromosome FASTA files on your computer.

$ gimme index /usr/share/genomes/hg19 hg19

Predict some motifs:

$ gimme motifs my_peaks.bed -g hg38 -n my_motifs

Help

• Check the FAQ for common issues.

• The preferred way to get support is through the Github issues page

• Finally, you can reach me by mail or Twitter.