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)
Install the following Python packages (e.g. using pip insall
)
- pysam
- pybedtools
- intspan
- biopython (for transcriptome analysis)
- ruffus (for TAP and TAP2)
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
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