When Galaxy reads and updates the integrated_tool_panel.xml file,
tools in multiple sections can be lost.
1) Install tool shed repository A into section A
<section id="A" name="A" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/some-user/repo-A/tool-A/
1.0.0" />
</section>
2) Install tool shed repository B into section B
<section id="A" name="A" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/some-user/repo-A/tool-A/
1.0.0" />
</section>
<section id="B" name="B" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/some-user/repo-B/tool-B/
1.0.0" />
</section>
3) Edit integrated_tool_panel.xml to put a tool from repository B
into section A
<section id="A" name="A" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/some-user/repo-A/tool-A/
1.0.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/some-user/repo-B/tool-B/
1.0.0" />
</section>
<section id="B" name="B" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/some-user/repo-B/tool-B/
1.0.0" />
</section>
4) When starting, tool-B will appear in both sections of the tool
panel. Upon restart, tool-B will only appear in section B.
This is due to a bug in the code which reads and re-writes the
integrated_tool_panel.xml file. I've commited (96a2ab47b882) to
galaxy-central a new version of lib/galaxy/tools/__init__.py which
includes a workaround for this issue.
Instead of my workaround, I would suggest some combination of:
a) adjusting init_tools() and called methods to get this right
b) redesigning the code and/or data structure used to read and
write integrated_tool_panel.xml
-rico
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