Hello, I have been exploring usegalaxy lately, and surprised to find out that there is no faidx, and CreateSequenceDictionary under samtool and picard, whereas many other tools are provided and available. I am confused as to why these tools are not provided, because many other sam, gatk tools would reply on their outputs to run correctly. Or they are there, i just did not find them. But, i have done scanning tool by tool, and searching, and not results. Any good answers or alternatives would be greatly appreciated. Thanks!
Not all intermediate processing datatypes are supported in the GUI because they are not needed. The tool wrappers themselves handle the files and just results are given back to the history as a dataset.
If you want to use your own custom genome with tools that require this index (and other metadata Galaxy uses), it is created and used this way: https://galaxyproject.org/learn/custom-genomes/
The GATK wrappers (all) are considered deprecated but could still be reviewed in the development repo linked from the tool's Tool Shed home page to understand how the data is modeled. These wrappers may be updated in the future but no firm plans are in place as far as I know. New datatypes could be created/added to your own Galaxy if you wanted to process/report the results differently when creating your own tool wrappers. Other tools that use indexes not needed in the GUI itself (to label datasets) could also be reviewed. https://usegalaxy.org/toolshed
Thanks! Jen, Galaxy team