Tool missing from Galaxy

First, restart Galaxy and watch the log for lines like:

Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/sickle/sickle/1.33, version: 1.33 into tool panel....

After startup, check integrated_tool_panel.xml for a line like the following to be sure it was loaded properly and added to the toolbox (if not, check the logs further)

<tool id="toolshed.g2.bx.psu.edu/repos/iuc/sickle/sickle/1.33" />

If it is a toolshed tool, check shed_tool_conf.xml for

<tool file="toolshed.g2.bx.psu.edu/repos/iuc/sickle/43e081d32f90/sickle/sickle.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/sickle/sickle/1.33">
...
</tool>

Additionally if you have multiple job handlers, sometimes, rarely they don’t all get the update. Just restart them if that’s the case. Alternatively you can send an (authenticated) API requested:

curl -X PUT https://galaxy.example.org/api/configuration

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