RNA STAR version 2.7.2b does not find natively indexed reference genomes

[jennaj]

The tool form is not finding the existing indexes. Only at usegalaxy.org. At usegalaxy.eu, the tool form does find prior existing indexes.

Problematic Tool: RNA STAR Gapped-read mapper for RNA-seq data (Galaxy Version 2.7.2b)

That version is the most current version in the ToolShed and what loads from the tool panel. https://toolshed.g2.bx.psu.edu/view/iuc/rgrnastar/b9e04854e2bb

Test history:

• https://usegalaxy.org/u/jen/h/test-rna-star-mapper
• Includes a test to see if an older version runs successfully as a temporary workaround.
• Update: confirmed, this version can be used instead:RNA STAR Gapped-read mapper for RNA-seq data (Galaxy Version 2.6.0b-1)

ping @natefoo @davebx @mvdbeek -- Is this the same as other problems due to the CVMFS updated data paths?

[jennaj]

Linking in Galaxy Help Q&A about the issue: https://help.galaxyproject.org/t/rna-star-reference-genome/3156

[jennaj]

Status for end-users:

• Please the Galaxy Help post above for ongoing community Q&A
• Follow for ongoing technical updates at a related ticket: RNA-Star 2.6.0b does not lists out indexed genomes on the tool form at usegalaxy.org #266

Closing this one out to consolidate all into one issue at this repo.