SnpEff, Trimmomatic, and FastQC tools require Java to be installed and specified in the UGENE Application Settings.
If a tool is specified in the Application Settings, but Java is not, an error message appears on validation of a workflow with such element. However, the corresponding message needs to be improved.
Scenario:
- Specify the correct SnpEff executable file in the Application Settings.
- Make a field for "java" executable empty in the Application Settings.
- Open the Workflow Designer.
- Add the "SnpEff Annotation and Filtration" element to the scene.
- Select the "Genome" parameter.
Current state: a message box appears with the following error message (see the attached screenshot):The list of SnpEff genomes is not available. Path for SnpEff is not selected. Do you you want to select it now?
Expected state: the message should be the following:
The list of genomes is not available. The SnpEff tool requires java that is not set. Do you want to select it now?