Error pushing tool to toolshed using planemo

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#1

Hello,
I am having a weird issue trying to push my tool (a wrapper for alevinQC) to the main toolshed. I used planemo to prepare my submission to the toolshed.

I have a working version on the test toolshed: https://testtoolshed.g2.bx.psu.edu/view/florian.wuennemann/alevinqc/49fe36f5ad92

I tried pushing to the main toolshed using planemo and it created an entry but somehow that entry is not findable by others in the toolshed and I can’t install it in my galaxy from the main toolshed:
https://toolshed.g2.bx.psu.edu/view/fwuennemann/alevinqc/000000000000

When I try to interact with the main toolshed entry via planemo, it tells me it doesn’t exist, but when I try to create a new toolshed entry, it tells me I own a tool with that name… (see code below)

Thanks for the help!

planemo shed_create --shed_target toolshed
Unexpected HTTP status code: 400: {"err_msg": "You already own a repository named <b>alevinqc<\/b>, please choose a different name.", "err_code": 400008}

planemo shed_diff --shed_target toolshed
shed_diff: Repository [alevinqc] does not exist in the targeted Tool Shed.

 planemo shed_update --check_diff --shed_target toolshed
Repository [alevinqc] does not exist in the targeted Tool Shed.
Failed to update repository 'alevinqc' as it does not exist on the main Tool Shed.
1 Like
#2

Hi @florian.wuenneman!

Can you please try planemo shed_upload --shed_target toolshed ./alevinqc/

Hope that works,
Bjoern

1 Like
#3

Thank you for the help, Bjoern!

I tried to run shed_upload inside the tool folder from my local machine and outside the folder specifying it. In both cases, it returned the following:

git rev-parse HEAD
galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
git diff --quiet
Repository [alevinqc] does not exist in the targeted Tool Shed.

Do you have any other suggestions?

Thanks,

Florian

#4

Appears to be something weird going on inside the toolshed - when I following this link on the toolshed to your repository found with a name search: https://toolshed.g2.bx.psu.edu/repository/browse_repositories?f-free-text-search=alevinqc&sort=name&operation=view_or_manage_repository&id=4ad514afab719a60
I see a strange cascade of windows - never seen that. Looks like the toolshed is in a state of confusion about that tool :frowning:

#5

Thanks for confirming that this weird cascading effect is going on in the toolshed @fubar !

I think because the upload of the tool to toolshed failed, it’s stuck in this state of having the entry but not having actual metadata associated with it. I can see something for this package when I am logged in to my toolshed account…

Is there a way to delete the current alevinqc from the main toolshed and just restart the process? @bjoern.gruening or anyone else familiar with the toolshed?

#6

I think this is a different bug due to the rewrite.

#7

Can you add --force_repository_creation to your command?

#8

Unfortunately, still getting an error:

git rev-parse HEAD
galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
git diff --quiet
Unexpected HTTP status code: 400: {"err_msg": "You already own a repository named <b>alevinqc<\/b>, please choose a different name.", "err_code": 400008}
Repository [alevinqc] does not exist in the targeted Tool Shed.
#9

Does anyone else have any other suggestions? It seems like I am stuck at this point unfortunately, unable to publish the tool on the main toolshed right now…

One idea is to just resubmit the tool with a slightly different name to make it work?
For example alevinqc_galaxy?

Thank you for the help everyone!

#10

The resubmitting with different repo name will most probably work. At this point I suspect the mercurial repository corresponding to your repo on the toolshed side is in a bad shape and needs some manual reset/fixing.

#11

I was finally able to fix this issue, by logging into the toolshed and uploading a tarball directly on the defective repo page for alevinqc. Now the entry seems to be correct and installable via toolshed. Any confirmation of correct install from a second source would be appreciated!
https://toolshed.g2.bx.psu.edu/view/fwuennemann/alevinqc/5f0da20666fa