How to set up public dataset analysis with bcbio-nextgen

We use bcbio-nextgen for the analysis of sequencing data, mainly, (sc)RNAseq, smallRNAseq, DNASeq and ChIPSeq. It is not rare that we get collaborators who wants to re-analyze public data-set. Inside bcbio, we have to help to merge multiple files that belong to the same sample into one file to make easier the configuration of bcbio. We extended this script to pull down data from GEO and SRA repository. If you have bcbio.