Installation & dependencies

Installation

The bap pipeline primarily relies on a Python3 package that contains most necessary information and meta data for downstream processing. Additional environmental tools and packages are required for functionality, which are outlined here.

Recommended: First, create a python virtual environment in some working directory to keep things tidy:

python3 -m venv venv3
source venv3/bin/activate

Next, install bap from PyPi:

pip install bap-atac

You can also

git clone https://github.com/caleblareau/bap.git
cd bap
pip3 install -e . 

Verify install:

bap2 --help

This should verify that the tool and the python package dependencies are all installed.

Additional requirements

In addition the python bap package, the following tools should be installed:

• R with packages GenomicRanges, ggplot2, data.table, and dplyr
• bedtools (v2.25+)
• samtools (v1.9+)
• bgzip
• tabix
• snakemake (which should be present as part of the bap installation)

Note: if you specify a valid file with --peak-file, a peaks x cell RangedSummarizedExperiment will be generated, meaning that the SummarizedExperiment package is also a dependency when using this flag.

Manually specify binaries

When possible, bap will find the following binary executables in your environment: R, bedtools, samtools, bgzip, tabix, and snakemake. If you want to manually specify which is being executed, you can use these command line parameters:

  --r-path TEXT                   Path to R; by default, assumes that R is in
                                  PATH
  --bedtools-path TEXT            Path to bedtools; by default, assumes that
                                  bedtools is in PATH
  --samtools-path TEXT            Path to samtools; by default, assumes that
                                  samtools is in PATH
  --bgzip-path TEXT               Path to bgzip; by default, assumes that
                                  bgzip is in PATH
  --tabix-path TEXT               Path to tabix; by default, assumes that
                                  tabix is in PATH
  --snakemake-path TEXT           Path to snakemake; by default, assumes that
                                  snakemake is in PATH