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).
[![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io)
[![PyPI version](https://badge.fury.io/py/gimmemotifs.svg)](https://badge.fury.io/py/gimmemotifs)
[![Build Status](https://travis-ci.org/simonvh/gimmemotifs.svg?branch=master)](https://travis-ci.org/simonvh/gimmemotifs)
[![Code Health](https://landscape.io/github/simonvh/gimmemotifs/master/landscape.svg?style=flat)](https://landscape.io/github/simonvh/gimmemotifs/master)
[![Documentation Status](https://readthedocs.org/projects/gimmemotifs/badge/?version=master)](http://gimmemotifs.readthedocs.io/en/master/?badge=master)
[![DOI](https://zenodo.org/badge/676678.svg)](https://zenodo.org/badge/latestdoi/676678)
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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