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