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Bowtie2 & HISAT2 test history: https://usegalaxy.org/u/jen/h/test-mappers-and-clusters
For the workaround until resolved, please see this Galaxy Help post: https://help.galaxyproject.org/t/hisat2-not-working/2189/7?u=jennaj
Reminder: Stampede should never be as a target cluster for any mapping jobs. Using default settings will not send jobs to that cluster, but it is possible to directly select that cluster on the tool form. Avoid Stampede or reliably expect the job to remain in the "queued" state and eventually fail. Prior ticket: #214
Note to all end users running mapping: Using all defaults for the "Job Resources" parameter is a good choice now again. No need to target a particular cluster anymore. Allowing Galaxy to choose the target cluster based on the currently available resources, at the time of job submission, is the fastest way to run tools.
All mapping tools are Ok except for RNA-Star when sent to PCS Bridges cluster.
@jmchilton thinks they need up update their version of Galaxy
@natefoo can you help?
For end-users: Workaround pending testing (in the same test history above). Checking to see if targeting the "Jetstream" or "Galaxy cluster" under the Job Resources option will run successful jobs (similar to the prior workaround included in the Galaxy Help post above).