gimmemotifs 0.12.0

GimmeMotifs is a motif prediction pipeline.

GimmeMotifs

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

Install GimmeMotifs:

$ conda install gimmemotifs

Or create a specific environment:

$ conda create -n gimme python=3 gimmemotifs

Python 3 is the preferred version, however, GimmeMotifs also supports Python 2. If you created a conda environment, don't forget to activate it with source activate gimme whenever you want to use GimmeMotifs.

Quick start

Predict some motifs:

$ gimme motifs my_peaks.bed -g /data/genomes/hg38/hg38.fa -n my_motifs

Download a genome

The example above assumes that you have the hg38 genome in /data/genomes/hg38/hg38.fa. GimmeMotifs can also use genomes installed by genomepy.

You can configure the directory where genomepy stores genomes by editing ~/.config/genomepy/genomepy.yaml

genome_dir: /data/genomes

To download a genome from UCSC:

$ genomepy install hg38 UCSC --annotation

Now you can specify this genome for GimmeMotifs by name.

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

Help

• Full documentation: http://gimmemotifs.readthedocs.io/.
• 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.