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"author": "Simon van Heeringen",
"author_email": "simon.vanheeringen@gmail.com",
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"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Operating System :: MacOS :: MacOS X",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python :: 2.7",
"Programming Language :: Python :: 3.5",
"Topic :: Scientific/Engineering :: Bio-Informatics"
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"description": "# GimmeMotifs\n\n[](http://bioconda.github.io)\n[](https://badge.fury.io/py/gimmemotifs)\n[](https://travis-ci.org/vanheeringen-lab/gimmemotifs)\n[](https://landscape.io/github/simonvh/gimmemotifs/master)\n[](http://gimmemotifs.readthedocs.io/en/master/?badge=master)\n\n[](https://zenodo.org/badge/latestdoi/676678)\n\nSuite of motif tools, including a motif prediction pipeline for ChIP-seq experiments.\n\nSee [full GimmeMotifs documentation](http://gimmemotifs.readthedocs.org/) for detailed installation instructions and usage examples.\n\nFor documentation on the development version see [here](http://gimmemotifs.readthedocs.org/en/latest/).\n\nThe manuscript describing this latest release is available on [biorRxiv](https://doi.org/10.1101/474403) as a preprint and can be cited as:\n\n> [**GimmeMotifs: an analysis framework for transcription factor motif analysis**](https://doi.org/10.1101/474403)
\nNiklas Bruse, Simon J. van Heeringen
\n_bioRxiv_ (2018) DOI: [10.1101/474403](https://doi.org/10.1101/474403)\n\n\n## We need your help!\n\nGimmeMotifs was originally developed for our own needs but we would really like it to be useful to the wider community. However, this also depends on your input. Let us know what you think! What features are missing? Which tutorial would you like to see? What part of the documentation is unclear? Have great ideas for future developments? Maybe you even want to join in developing this software?\n\n[Let us know!](https://github.com/simonvh/gimmemotifs/issues/)\n\n\n\n## Easy installation\n\nThe most straightforward way to install GimmeMotifs is via [conda](https://docs.continuum.io/anaconda/) using the [bioconda](https://bioconda.github.io/) channel.\n\nIf you have not used bioconda before, first set up the necessary channels (in this order!). You only have to do this once.\n\n```\n$ conda config --add channels defaults\n$ conda config --add channels bioconda\n$ conda config --add channels conda-forge\n```\n\nYou can now install GimmeMotifs with one command:\n\n```\n# Create an environment called gimme with all dependencies\n$ conda create -n gimme python=3 gimmemotifs\n\n# Activate the environment\n$ conda activate gimme\n```\n\nPython 3 is the required, from version 0.13.0 on GimmeMotifs no longer supports Python 2. \nDon't forget to activate the environment with `conda activate gimme` whenever you want to use GimmeMotifs.\n\n## Quick start\n\n### Predict some motifs:\n\n`$ gimme motifs my_peaks.bed -g /data/genomes/hg38/hg38.fa -n my_motifs`\n\n### Download a genome\n\nThe example above assumes that you have the hg38 genome in\n`/data/genomes/hg38/hg38.fa`. \nGimmeMotifs can also use genomes installed by\n[genomepy](http://github.com/simonvh/genomepy).\n\nYou can configure the directory where genomepy stores genomes by editing\n`~/.config/genomepy/genomepy.yaml`\n\n``` \ngenome_dir: /data/genomes\n``` \n\nTo download a genome from UCSC:\n\n`$ genomepy install hg38 UCSC --annotation`\n\nNow you can specify this genome for GimmeMotifs by name.\n\n`$ gimme motifs my_peaks.bed -g hg38 -n my_motifs`\n\n\n## Help \n\n\n* Full documentation:\n [http://gimmemotifs.readthedocs.io/](http://gimmemotifs.readthedocs.io/).\n* Check the [FAQ](http://gimmemotifs.readthedocs.io/en/master/faq.html#faq) for\n common issues.\n* The preferred way to get support is through the Github\n [issues](https://github.com/simonvh/gimmemotifs/issues/) page\n* Finally, you can reach me by [mail](simon.vanheeringen@gmail.com) or\n [Twitter](https://twitter.com/svheeringen).",
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