required_docker_tools.txt

####################################################################################################
##   All docker tools are available at dockerhub/aarjunrao (hence the default dockerhub in the    ##
##   config yaml is aarjunrao). The Dockerfiles used to generate all docker images is available   ##
##   at https://www.github.com/arkal/dockernator                                                  ##
####################################################################################################

# Alignment
	cutadapt:1.9.1
	bwa:0.7.9a
	star:2.5.2b
	starlong:2.4.2a

# Alignment post
	samtools:1.2
	picard:1.135

# Expression Estimation
	rsem:1.2.20

# Haplotyping
	phlat:1.0

# Mutation Calling
	mutect:1.1.7
	radia:bcda721fc1f9c28d8b9224c2f95c440759cd3a03
	filterradia:bcda721fc1f9c28d8b9224c2f95c440759cd3a03
	muse:1.0rc_submission_b391201
	somaticsniper:1.0.4
	somaticsniper-addons:1.0.4
	samtools:0.1.8
	strelka:1.0.15
	bam-readcount:0.7.4

# Mutation Annotation
	snpeff:3.6

# Mutation Translation
	transgene:2.3.2

# MHC:peptide binding prediction
	mhci:2.13
	mhcii:2.13
	netmhciipan:3.1

# Prediction Ranking
	rankboost:2.1.4