Tallyup: the Docker pipeline driving the Digital Expression Explorer 2 resource

Digital Expression Explorer 2 is among the most comprehensive gene expression datasets currently available (http://dee2.io/; DOI:10.1093/gigascience/giz022). Underlying this massive dataset is a software pipeline that acquires transcriptome sequencing data from NCBI's Sequence Read Archive, processes and summarises this data into counts that can be readily used in subsequent analysis. The motivation for this submission is to indefinitely archive this pipeline, which was previously hosted at DockerHub. In order to use this Docker image, run the following commands on a linux computer:

# uncompress the file
gunzip tallyup.tar.gz

# load into docker
docker load < tallyup.tar

# test with a small dataset 
docker run mziemann/tallyup ecoli SRR057751