I've had a Galaxy instance running for some time now and many tools have been updated. Recently, however, I've started running into issues where multiple versions of tools are not being displayed properly in the tool menu.

Tophat2 example:

I have the original tophat2 (bundled with Galaxy), and versions 0.6, 0.7, and 0.9 installed. The tool lineage looks fine (see below), however, I end up with two tools listed in the toolbar. One defaults to version 0.9 and allows me to switch to 0.6 or 0.7. The other defaults to version 0.6 and does not show any other versions. This is happening with many tools for me and is quite frustrating, and in some cases, very confusing.

Can anyone hlep shed light on how the tool menu is generated and where I might look to resolve some of these issues? Thanks in advance for any help.

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.6>
        
tophat2 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.6>

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.6>

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.6>

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.6>

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.7>
        
tophat2 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.7>

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.7>

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.7>

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.7>

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.9>
        
tophat2 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.9>

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.9>

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.9>

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9 <https://galaxy.princeton.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ftophat2%2Ftophat2%2F0.9>

tophat2 <https://galaxy.princeton.edu/tool_runner?tool_id=tophat2>
        
tophat2 <https://galaxy.princeton.edu/tool_runner?tool_id=tophat2>

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6 <https://galaxy.princeton.edu/tool_runner?tool_id=tophat2>

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7 <https://galaxy.princeton.edu/tool_runner?tool_id=tophat2>

toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9 <https://galaxy.princeton.edu/tool_runner?tool_id=tophat2>




--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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