Trouble finding (and installing) tools from testtoolshed

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1

Dear all,

I am having trouble deploying my tools on testtoolshed for final test befor submitted them on the toolshed. The 3 tools are available on testtoolshed :

But when looking for them trough de Galaxy Admin interface I can only find frogs_core. This is the same when exploring the testtoolshed using tool name, but you can find the 3 of them if you explore testtoolshed via Metagenomics category and then filter by frogs term, or if you explore tools with owner == oinizan. All code are available on github : https://github.com/geraldinepascal/FROGS-wrappers/tree/dev (dev branch).

Does anyone know why this happens?

2

For information, I succeed to install the 3 tools via ephemeris. I guess that this it could be a bug in testtoolshed…

3

Hi @mariabernard

A direct search like this one. → Galaxy Tool Shed also misses the Frogs_func and Frogs_stat tools.

I don’t see anything obvious so let’s get some feedback from the developers! This is the link to my question at Matrix but let’s keep the conversation here, they’ll post back to this thread.

More soon! :slight_smile:

4

It seems that nobody knows…

I have an other problem. As all my tests passed, I attempt to submit these new tools on toolshed.

`planemo shed_create --shed_target toolshed`

It did not produce any error, but neither any successful message and finally I have now a frogs_core repository (owner frogs) but which is empty.

I don’t what to do now. I did not test with the other tools as I am not sure of the consequences of the empty repository submission…

Does any one can help, or do you now where I can find help ?

Best regards

(I will be away until March… but another colleague will follow this discussion)

5

Hi @mariabernard

After reviewing conversations on the dev matrix over the last few days, it seems the team is in the middle of freezing the next release. Now, this wouldn’t usually mean the test toolshed is impacted (when using the existing dev branch instance) but I can see that others have had some small issues and delays. In particular, some CLI processes and GH actions today. But this is all performance and doesn’t really explain the empty result.

So, for this issue specially, and considering the prior repositories that seem to be unlisted..

I see what I think is your latest repository. → Galaxy Tool Shed

I’m wondering if there is some problem with the shed.yml configuration file? Would you like to compare to the templates here? Just to make sure your configurations are current?

Planemo (probably Ok given your result so far)

Tool package. These are the instructions Planemo follows to publish a repository into a tool shed. Missing content could indicate a problem with these instructions.

For the tool you loaded today, this is the file

Then, just as a comparison, please see these

The first item I notice is the multi-line format for long_description. Using the pipe instead of single quotes is where I would suggest starting. After, I would suggest removing any other extra single quotes, reformatting the categories (may help to get this listed!), and deciding if you need a .lint_skip file.

The IUC may be able to help more with the organization overall. Example: should these be labeled as a suite? If you have specific question, you can ask here and we can ping them that way too. :slight_smile: