Software

This is a list of software that is being installed when you use this image. If you have any issues using this playbook on a deNBI virtual machine or any other system, please write an issue.

software	command line
Miniconda	conda
Pangenie	PanGenie, Pangenie-graph
Minimap2	minimap2
Miniasm	miniasm
Minigraph	minigraph
vg	vg
odgi	odgi
graphtyper2	graphtyper
Bandage	Bandage
Seqwish	seqwish
Gfaffix	gfaffix
Smoothxg	smoothxg
Wfmash	wfmash
Pggb	pggb
IGV	IGV
Cactus	see below
RTG Tools	/home/ubuntu/rtg-tools-3.12.1/rtg
SnpEff	java -jar /home/ubuntu/snpEff/snpEff.jar
ClinEff	java -jar /home/ubuntu/clinEff/ClinEff.jar
Gfaffix	gfaffix

All software with exception of cactus is available directly from the command line. You can see all executables in /usr/local/bin/. Cactus has its own environment because it comes packaged with its own version of some of the software in the list. In order to use cactus and the versions of the software that cactus relies on, activate the conda environment conda activate cactus.

Bandage and IGV are GUI software. This playbook also installs an X-server which can be used via ssh when you provide the -X parameter.

Acknowledgements

Funding provided by the BMBF - Förderkennzeichen 031L0184B.