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/activate

The installation can then be specified using the following:

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/activate
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.

Installing proatac as an environment module.

A common use case of proatac will be processing ATAC-seq data in a high-performance computing cluster environment. As each computing cluster is different, you’re probably best off inquiring with you sysadmin how to install proatac Here are a few general tips though (modified from the MultiQC installation guide):

A typical installation procedure with an environment module Python install might look like this: (Note that $PYTHONPATH must be defined before pip installation; this can be specified by creating a virtual environment and loading it as shown above)

# Create the proatac version (replace 0.3 with whatever the current version is)
VERSION=0.3
INST=/path/to/software/proatac/$VERSION
module load python/3.6.1
mkdir $INST
export PYTHONPATH=$INST/lib/python3.6/site-packages
pip3 install --install-option="--prefix=$INST" multiqc

Once proatac is installed, we need to create a new module file. While these vary between systems, but here’s an example that also imports the necessary dependencies:

#%Module1.0#####################################################################
##
## proatac
##

set components [ file split [ module-info name ] ]
set version [ lindex $components 1 ]
set modroot /path/to/software/proatac/$version

proc ModulesHelp { } {
    global version modroot
    puts stderr "\proatac - use proatac $version"
    puts stderr "\n\tVersion $version\n"
}
module-whatis   "Loads proatac environment."

# load required modules
module load python/3.6.1
module load samtools/1.5.0
module load R/3.4.0
module load java/1.6.0
module load macs2/2.1.1.20160309
module load bowtie2/2.3.1

# only one version at a time
conflict proatac

# Make the directories available
prepend-path    PYTHONPATH  $modroot/lib/python3.6/site-packages