Irida pipelines dumped to top level menu

phac-nml / irida

Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology

https://irida.ca

Apache License 2.0

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Irida pipelines dumped to top level menu #225

Closed happykhan closed 5 years ago

happykhan commented 5 years ago

Most of the other galaxy tools are set up under headers e.g.

Annotation

Prokka Prokaryotic genome annotation
MOB-Recon Type contigs and extract plasmid sequences
MOB-Typer Get the plasmid type and mobility given its sequence
ABRicate Mass screening of contigs for antimicrobial and virulence genes
ABRicate List List all of abricate's available databases.

When I used install_tool_shed_tools.py It seems to have put everything at the top level which is a lot of clutter. How do I fix this (move tools into groups) and have pipelines not do this in the first place.

screenshot from 2018-12-17 14-31-17

apetkau commented 5 years ago

Thanks for reporting this. There is a parameter to install_tool_shed_tools.py (--section TOOL_PANEL_SECTION_ID) which you can use to group the tools, but this will group all of them into a single category. I will look into setting up some default categories for the IRIDA tools.

For organizing them after install, I you can do this by editing the file integrated_tool_panel.xml to group the tools into sections (https://docs.galaxyproject.org/en/master/admin/tool_panel.html#layout).

happykhan commented 5 years ago

Organizing after install i had to edit shed_tool_conf.xml (Galaxy v 18) integrated_tool_panel is rebuilt on server restart (so changing this file is always overwritten).