Tools registered with testtoolshed.g2.bx.psu.edu cannot be installed

1

Hi, all

I can’t install the tools registered on testtoolshed.g2.bx.psu.edu.
When I go to https://testtoolshed.g2.bx.psu.edu/ site in my web browser and click on the Contents button I get an error message “Mercurial repository not found”.

Other tools also show the same error on the website.

Thanks.

2

Welcome, @youyuh48

The service appears to be up, and no recent downtime has been reported according to → https://status.galaxyproject.org/

Maybe the repository itself has some issue.

Some ideas:

  • If the target tool is in the Main ToolShed, source it from there instead
  • If this was your own test repository, maybe there was some problem setting it up?

You can explain with more context about what is going on.

Is this a new server?
Have you successfully installed tools from a ToolShed before?
What version of Galaxy are you running?
Anything else you think might be relevant…

XREF: Development in Galaxy / Tutorial List

Thanks! :slight_smile:

3

@jennaj Thanks for the reply. I am using Galaxy version 21.09 installed on Linux and have successfully installed several tools from ToolShed.

Here is the error log when I installed the tools I registered myself in the “testtoolshed” repository.

$ tail -n 10000 galaxy.log  | grep combine_bracken_outputs | grep hg

galaxy.tool_shed.util.hg_util ERROR 2024-07-16 12:15:36,267 [pN:main.web.1,p:8773,w:1,m:0,tN:uWSGIWorker1Core1] Error cloning repository: Command '['hg', 'clone', '-r', '0', 'https://testtoolshed.g2.bx.psu.edu/repos/youyuh48/combine_bracken_outputs', '/home/galaxy/galaxy/database/shed_tools/testtoolshed.g2.bx.psu.edu/repos/youyuh48/combine_bracken_outputs/6e90a30b214f/combine_bracken_outputs']' returned non-zero exit status 255.

I think there is something wrong with the “testtoolshed” repository, because https://testtoolshed.g2.bx.psu.edu/repositories/d4acd659ee3bd7e4 iuc’s minimap2, which is also registered in the “testtoolshed” repository, failed to install with the same error.

Also, when I clicked on the “Contenets” button on the website of the following repository, I got the error message “Mercurial repository not found The specified repository “repos/iuc/minimap2/rev/tip” is unknown, sorry. Please go back to the main repository list page. Please go back to the main repository list page.”

I appreciate your help in resolving this issue.

5

Hi @youyuh48

I just checked with the administrators, and the advice is, that unless you are working on a development project, the Test ToolShed (TTS) should be avoided.

If that is what you are doing, development would involve the use of a Galaxy server running a more current development or production version of Galaxy, not an older release. See → https://docs.galaxyproject.org/en/master/releases/index.html

If a tool you want to use is only hosted in the TTS, it might not be ready to be used. You could reach out to the authors and ask about the status if something is not clear about why it isn’t in the Main ToolShed.

If you use case is different, you can explain more. Thanks! :slight_smile:

6

Hi @jennaj

I appreciate you checking with the admin. I am doing tool development work on Docker Galaxy Stable and older versions of Galaxy, but I don’t have enough time to upgrade to the latest Galaxy anytime soon.

Could you please provide me with the URL of any documentation on how to register (or request) the XML of my own tool development to the Main Tool Shed?

Thank you. :grinning:

7

Hi @youyuh48

Thanks for explaining, please see → https://planemo.readthedocs.io/

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