A bit more tracing leads me to suspect that what is happening is that a merge is being called here:




i.e. the toolshed maintains an in-memory copy of tool-data tables and if the list of columns in an incoming tool-data table is not the same as the in-memory version the error I saw happens.

Which leaves me with the question: how is one meant to update the column list of a tool data table?


On Mon, 17 Sep 2018 at 13:23 Peter van Heusden <pvh@sanbi.ac.za> wrote:
Thanks - which is probably because of the previous failures with `shed_update` - which relate back to the topic of my original email. I suspect that failure from `planemo shed_update` has led to this "not installable" state. And I don't know how to solve the problem from `shed_update` which *looks* like it is coming from a clash between previous and current definitions of the tool-data table.


On Mon, 17 Sep 2018 at 12:58 Nicola Soranzo <nicola.soranzo@gmail.com> wrote:
Hi Peter,
if you open the page for data_manager_shapeit_reference in the test ToolShed you will see that revision 5 and 6 are not installable, they both have "This revision can be installed: False" . If you instead select revision 3 it is installable.


On 17/09/18 11:51, Peter van Heusden wrote:
I'm following up on my previous email. I somehow managed to get `planemo shed_update` to work but now I seem to have an inconsistent view of the Test toolshed. This is how it looks from the Admin panel of my Galaxy server:

Notice that it shows 3 installable revisions for the data manager, last updated 13th of September. And this is how it looks from the Test toolshed website:


Notice that it has 6 installabale revisions for the data manager. Is my Galaxy server perhaps caching something?


On Sat, 15 Sep 2018 at 09:57 Peter van Heusden <pvh@sanbi.ac.za> wrote:
Hi there

I'm working on a data manager to keep track of the reference data collection used by the SHAPEIT2 tool. I had to add a column to the data manager but when I try and do a `planemo shed_update` I get the error:

Unexpected HTTP status code: 500: {"err_msg": "Error attempting to parse file tool_data_table_conf.xml.sample: Merging tabular data tables with non matching columns is not allowed: shapeit_ref:{'path': 2, 'reference_prefix': 3, 'name': 1, 'value': 0, 'map_prefix': 4} != shapeit_ref:{'name': 1, 'value': 0, 'sample_prefix': 5, 'path': 2, 'reference_prefix': 3, 'map_prefix': 4}"}

This is for data_manager_shapeit_reference in testtoolshed, which is on github at

As far as I can tell the columns do accord. Is there any way to see which files are being merged to help try and debug this error?


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