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GimmeMotifs is a motif prediction pipeline.

Project description

# GimmeMotifs

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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 before, first set up the necessary channels (in this order!). You only have to do this once.

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

You can now install GimmeMotifs with one command:

```
# Create an environment called gimme with all dependencies
$ conda create -n gimme python=3 gimmemotifs

# Activate the environment
$ conda activate gimme
```

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

### 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](http://github.com/simonvh/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/](http://gimmemotifs.readthedocs.io/).
* Check the [FAQ](http://gimmemotifs.readthedocs.io/en/master/faq.html#faq) for
common issues.
* The preferred way to get support is through the Github
[issues](https://github.com/simonvh/gimmemotifs/issues/) page
* Finally, you can reach me by [mail](simon.vanheeringen@gmail.com) or
[Twitter](https://twitter.com/svheeringen).

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