Hello
I am new to Galaxy
A student asked me to add a database from silva to galaxy
I downloaded the database but I dont know how to add it to our Galaxy site
Thanks
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Hello,
I think the forum members here need a bit more info if they want to help you. For which tool you want to use Silva? Like, BLAST or a mapper. Are you running galaxy local or are you using usegalaxy.org?
Maybe already some inspiration for you:
You can upload the fasta file by clicking the upload button on top of the tool menu. After that you can create a database with the makeblastdb tool. And after creating the database you can you use the blastn tool.
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Hello
I want to add an arb file from this link https://www.arb-silva.de/download/arb-files/
In a local Galaxy
Details always help. Is the use for this tool?
- SINA reference based multiple sequence alignment
- ToolShed repository to install to Galaxy: https://toolshed.g2.bx.psu.edu/view/iuc/sina/482052b30b78
- Development Repository with indexing help: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina
The tool form states that it accepts both fasta and arb reference datasets from the history. I haven’t tested that but you could try. Or, pre-index your data to conserve memory usage during runtime – likely an important factor with this particular tool.
Contact the tool authors if you have indexing problems – either at the Github repo (an issue is best if you find an actual bug) or ask for more help/vet a question at Gitter here: https://gitter.im/galaxy-iuc/iuc
Please review and clarify more about your goal if this is not your use case.
Thanks @gbbio!!
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