INSTALL.md

Dependencies

Software

Make sure the following software are in your PATH

• bwa
• samtools
• blastn
• gmap (for Fusion-Bloom, TAP, TAP2)
• biobloomtools (for TAP and TAP2)
• RNA-Bloom (for Fusion-Bloom and TAP2)
• Trans-ABySS (for TAP)

Python package

Install the following Python packages (e.g. using pip insall)

• pysam
• pybedtools
• intspan
• biopython (for transcriptome analysis)
• ruffus (for TAP and TAP2)

Install PAVFinder in a conda environment

conda create -n pavfinder
conda activate pavfinder
conda install -c bioconda pavfinder

It is recommended to use mamba instead of conda, i.e.

mamba install -c bioconda pavfinder

Install PAVFinder in virtualenv

This is an alternative to using a conda environment. All required software listed above must be in your PATH.

$ pip install virtualenv
$ virtualenv <DIR>
$ source <DIR>/bin/activate
$ pip install git+https://github.com/bcgsc/pavfinder.git#egg=pavfinder