Mark as deprecated at usegalaxy.org: Velvet[h|g] and VelvetOptimiser (all versions)

[Jennifer Hillman-Jackson]

Notice for end-users: Upgrade to SPAdes for analysis purposes

Velvet related tools are older, and some have datatype requirements that differ from more current tools. Some users have reported that earlier versions of these tools (the same version as included in the GTN tutorials they are following) work fine, so that may be an option if you really want to follow an existing GTN tutorial (linked below).

• Avoid Velvetg and Velveth when possible. If used for training, and fastq inputs are involved, these must be assigned the datatype fastq. Input with the datatypefastqsanger will fail. Medium to large assemblies will fail for resources.
• Use VelvetOptimiser for training purposes only. This tool does accept inputs with the fastqsanger datatype. Medium to large assemblies will fail for resources.

GTN tutorials: https://training.galaxyproject.org/training-material/topics/assembly/

• Velvetg and Velveth: https://training.galaxyproject.org/training-material/topics/assembly/tutorials/general-introduction/tutorial.html
• VelvetOptimiser and SPAdes: https://training.galaxyproject.org/training-material/topics/assembly/tutorials/debruijn-graph-assembly/tutorial.html

Admin changes per @mschatz

1. Tag each of the three tools as deprecated (all versions)
2. Move into the "Deprecated/Assembly" section of the tool panel at usegalaxy.org
3. Prevent any future updates from removing the "deprecated" tags or moving the tool panel placement ongoing

Reported to galaxy-bugs mailing list, and at Galaxy Help: https://help.galaxyproject.org/t/galaxy-error-using-velveth-error-deprecated-tool-suite-try-spades-instead/5050.

[Jennifer Hillman-Jackson]

Those three tools show up with the deprecated tag now. Are under the Assembly tool group. I think that is fine. Thank you both!