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usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
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wrapper for amrplusplus #88

Open tothuhien opened 1 year ago

tothuhien commented 1 year ago

This tool: https://github.com/cdeanj/amrplusplus is a nextflow pipeline could be used in the IBA course if we call install it on usegalay.no. It has option to run with docker, but in theory could be run without docker by changing the nextflow.config file. I still have problem of simply running the workflow.

kjellp commented 1 year ago

This can maybe be useful background: https://github.com/nextflow-io/nextflow/discussions/3177

tothuhien commented 1 year ago

it seems that toolshed of NTNU is down. Where can I put the wrapper to test?

kjetilkl commented 1 year ago

I guess the best choice would be the official test-toolshed at https://testtoolshed.g2.bx.psu.edu. I have also temporarily moved the NeLS Tool Shed to our test server at https://test.usegalaxy.no/toolshed_nels, although that one is expected to be unstable. Of course, depending on where you are testing your tool, you could also copy the wrapper files directly to a Galaxy server and adding a line to one of the tool_config_files specified in the main galaxy.yml configuration file.

tothuhien commented 1 year ago

Thanks, I will look at those.