Thanks for sending the bug report in – reviewing.
Update 1: Other tests still running to address the path problem, but the gtf is also problem. The chromosome identifiers are a mismatch with UCSC’s rn6 genome chromosomes. The FAQ I linked before will help to get that corrected. UCSC has a version (linked in FAQ), as does Gencode for GRCm38/rn6 here: https://www.gencodegenes.org/mouse/. If you get the Gencode version, you’ll need to remove the header lines. Many topics cover it, this is a good one (refers to human but the same instructions apply to mouse): Wrong! Update 9/15/20: For rn6 UCSC does not have GTF in the right format (why explained here: Help for Differential Expression Analysis - Galaxy Community Hub) and Gencode does not have it at all (only human/mouse are supported).
But iGenomes does – scroll down in the topic below for instructions about how to get the data into Galaxy from that data provider. Or, you may be able to convert the identifiers in the current GTF with this tool Replace column by values which are defined in a convert file (Galaxy Version 0.2). One source for “convert files” is linked on that tool form, scroll down into the help. You probably want this file Rnor_6.0_ensembl2UCSC.txt – and the “raw” URL for that data here should be good to paste into the Upload tool without any manipulations re format/datatype: https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/b2862c4897cbe43f731e2cd6a2fdd2588b4e49b0/Rnor_6.0_ensembl2UCSC.txt. You can test either method out and use the resulting GTF with HISAT2 to see if it is complete/correct.
Update 2: Execution issues with RNA-Star are confirmed. An alternative tool is HISAT2. Issue ticket (will close out once fixed): Jetstream: Fails RNA-STAR 2.7.5b · Issue #306 · galaxyproject/usegalaxy-playbook · GitHub