A tool that's not available on Galaxy EU

usegalaxy.eu support
1

Hi,

I’d like to run the tool quarTeT GapFiller v1.2.1 with a scaffolded assembly and ONT reads as input, but i can’t find the tool anywhere on the Galaxy system (this may be my fault). What are my options? Ideally, I’d like this tool to be part of a workflow I’m building.

Thanks!

Ken.

2

Dear ProfKenNorris,

It seems to me there is no Galaxy tool for now to execute quarTeT commands. If you want to execute such command into a Galaxy workflow, wihtout creating a classical Galaxy tool, a possibility is to execute a Jupyter Notebook installing and allowing to execute quarTeT commands. Just to help, I created such a Jupyter Notebook from within Galaxy (using Galaxy JupyterLab tool), availbale there https://ecology.usegalaxy.eu/api/datasets/26c75dcccb616ac831c44b3841f32152/display?to_ext=ipynb, so you can use it to execute gapfiller from the JupyterLab launched from within Galaxy interactively, and/or execute the final Jupyter Notebook (dealing with input datasets and executing exactly the gapfiller with parameters you want) in batch mode, and if you want, in a workflow.