Question: question about indexing reference genome with Galaxy
gravatar for mark_eagle_lin
10 months ago by
mark_eagle_lin0 wrote:

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!

galaxy • 266 views
ADD COMMENTlink modified 10 months ago by Jennifer Hillman Jackson25k • written 10 months ago by mark_eagle_lin0
gravatar for Jennifer Hillman Jackson
10 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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:

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.

Development FAQs: - -

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 10 months ago • written 10 months ago by Jennifer Hillman Jackson25k
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