FreeBayes requires both: input with assigned database AND tool form selection of genome

[jennaj]

Tool

FreeBayes - bayesian genetic variant detector (Galaxy Version 0.4.1)

Problem

Job failures with errors that are unclear to users.

Suggested fix: do not require database metadata for inputs

Input coming from a workflow will not always have the database assignment. Earlier versions of the tool (or the tool as run in the most current Galaxy 16.07) did not have this requirement. Assigning genome build on the tool form was enough.

Workaround

Assign the database as a post-build action for the upstream tools within workflow editor. This makes the workflow itself intact.

[jennaj]

Retest in progress with version FreeBayes bayesian genetic variant detector (Galaxy Version 1.0.2.29-3). Works on standard input. This is probably enough for now.

The updated version of the tool will still fail when the input BAMs do not have a genome assigned (even though one is specified on the tool form). BUT the tool cannot be submitted without that content and the new version of the tool form has a good warning.

Usage update: If you are using an older workflow, it may need to be adjusted to have database assigned to the inputs. This database assignment can be a natively indexed genome database or a custom genome's build database. FAQ: https://galaxyproject.org/learn/custom-genomes/#custom-builds