gimmemotifs 0.11.0b0

GimmeMotifs is a motif prediction pipeline.

# GimmeMotifs

[](http://bioconda.github.io) [](https://badge.fury.io/py/gimmemotifs) [](https://travis-ci.org/simonvh/gimmemotifs) [](https://landscape.io/github/simonvh/gimmemotifs/master) [](http://gimmemotifs.readthedocs.io/en/stable/?badge=stable)

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

See [full GimmeMotifs documentation](http://gimmemotifs.readthedocs.org/) for detailed installation instructions and usage examples.

For documentation on the development version see [here](http://gimmemotifs.readthedocs.org/en/latest/).

## Easy installation

The most straightforward way to install GimmeMotifs is via [conda](https://docs.continuum.io/anaconda/) using the [bioconda](https://bioconda.github.io/) 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 `

Now you can create a new environment for GimmeMotifs:

$ conda create -n gimme python=3 gimmemotifs=0.11.0b0

Before using GimmeMotifs activate the environment:

$ source activate gimme

## 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

## Frequently Asked Questions (FAQ)

#### I get the following error: “Invalid value for background argument”.

Currently, this is a bug in the default configuration file. Run gimme motifs with the additional argument -b gc,random.