About¶
proatac is an open-source command-line toolkit that performs robust and scalable preprocessing of ATAC-Seq data. Specifically, we’ve implemented our workflow using
Installation¶
Install stable version through PyPi¶
There are a few dependencies needed to get proatac to run. All are very common bioinformatics tools / languages and should be readily available in most systems. However, note that the current implementation of proatac is not supported on Windows platforms.
Depending on your python environment, we generally recommend using a virtual environment
to keep python dependencies tidy. An example of installing proatac inside a new
python virtual environment called venv3 using the following sequence of commands–
python3 -m venv venv3
source venv3/bin/active
pip3 install proatac
Install via GitHub¶
Though not recommended, a bleeding-edge (development) version can be installed directly from Git. Again using a virtual environment–
python3 -m venv venv3
source venv3/bin/active
pip3 install git+ssh://git@github.com/buenrostrolab/search/tree/master/proatac
While installing proatac is obviously a great first step, make sure that all of the dependencies are met. Check out the next page for more detail.
Dependencies¶
Getting proatac running¶
proatac has a few dependencies that are listed below with relevant hyperlinks for
installation instructions from the source. To quickly determine what may be lacking in
your system, try running proatac with the default.yaml file
(more on that here) using the --check flag. To do this, we’ll first clone
the repository
git clone https://github.com/buenrostrolab/proatac.git
proatac yaml/default --check
If you get a message saying that the check was succesful, then you’re most likely ready to begin analyzing data. However, if you run into one or more error messages, you are likely missing the necessarily software. Make sure that
- bedtools
- bowtie2 and relevant index for analysis.
- java language
- macs2
We note that macs2 though also a PyPi package is only compatible with Python 2.7 whereas proatac is a Python 3 package. There’s a good chance that macs2 is already living in your environment if you are reading this help page, which can be tested using the following–
which macs2
and hopefully seeing a valid path. If not, one solution for macs2 install is to create a separate python2 virtual environment using the following commands –
python2 -m venv venv2
source venv2/bin/active
pip install numpy
pip install wheel
pip install macs2
- R language and package dependencies (see wiki/Rpackages for more information).
- samtools
Author¶
The primary developer is Caleb Lareau in the Buenrostro Lab.
Citation¶
If you use proatac in your research, please cite our tool at the following URL:
http://buenrostrolab.com/proatac
Bugs / Errors¶
Please let us know if you find any errors/inconsistencies in the documentation or code by filing a new Github Issue.
