FindSVSingularity

Singularity container for the FindSV pipeline. Use the following command to download the container

singularity pull --name FindSV.simg shub://J35P312/FindSVSingularity

Contains

TIDDIT

SVDB

Genmod

Nextflow

samtools

CNVnator

python 2.7, including all modules for running FINDSV

Usage

The environment is installed when running the FindSV install script. And the various package are run using FIndSV.

You may run any of the included packages manually:

singularity exec samtools 

singularity exec FindSV.simg genmod

singularity exec FindSV.simg svdb

singularity exec FindSV.simg /opt/CNVnator_v0.3.3/src/cnvnator

singularity exec FindSV.simg python

singularity exec FindSV.simg python /opt/TIDDIT/TIDDIT.py

To be added

These modules still needs to be added

VEP

manta

You need to install these modules yourself to run FindSV!