Hi Marius,
Also there is a discrepancy between the `name` you're using in the
.shed.yml and the name as displayed in the
toolshed, that is probably another issue to look at.
That was the problem. Thanks a lot. Can the name of the owner be freely
chosen? I remember that I specified a username when registering, but I
could not remember (and could not find a way to find this information on
the toolshed page).
Best,
Matthias
On 18 December 2017 at 10:49, Matthias Bernt <[email protected]> wrote:
Dear peter,
thanks for your comments. I tried to update:
`planemo shed_update --shed_target testtoolshed`
But planemo also complains about non existent repository:
```
Repository [fasta_regex_finder] does not exist in the targeted Tool Shed.
Failed to update repository 'fasta_regex_finder' as it does not exist on the
test Tool Shed
```
Cheers,
Matthias
On 18.12.2017 10:45, Peter Briggs wrote:
Hello Matthias
My reading of the planemo docs it was that "shed_create" just made the
repository, and that it had to be followed by the "shed_update" command in
order to upload the actual content. (The documentation could probably be
clearer on this I think.)
I'm not sure about the error from "shed_diff", maybe related to the
repository not having any content.
Best wishes
Peter
--
Peter Briggs [email protected]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
________________________________________
From: galaxy-dev [[email protected]] on behalf of
Matthias Bernt [[email protected]]
Sent: Monday, December 18, 2017 9:37 AM
To: Galaxy Dev List
Subject: [galaxy-dev] tool publishing
Dear dev-list,
I'm just trying to publish my first tool to the testtoolshed via
planemo. I got some problem during the process. Maybe someone can
kickstart me (I guess I just forgot something).
I followed http://planemo.readthedocs.io/en/latest/publishing.html
The step
`planemo shed_create --shed_target testtoolshed`
```
Repository created
cd '/home/berntm/projects/mb-galaxy-tools/fasta_regex_finder' && git
rev-parse HEAD
cd '/home/berntm/projects/mb-galaxy-tools/fasta_regex_finder' && git
diff --quiet
Repository [fasta_regex_finder] does not exist in the targeted Tool Shed.
```
When I check online the repository is there but no changeset seems
available. Retrying fails (expected):
`planemo shed_create --shed_target testtoolshed`
```
Unexpected HTTP status code: 400: {"err_msg": "You already own a
repository named <b>fasta_regex_finder<\/b>, please choose a different
name.", "err_code": 400008}
````
Also shed_diff fails
`fasta_regex_finder git:(master) ✗ planemo shed_diff --shed_target
testtoolshed`
```
shed_diff: Repository [fasta_regex_finder] does not exist in the
targeted Tool Shed.
```
Any idea?
Cheers,
Matthias
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
[email protected], www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
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--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
[email protected], www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig
Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
[email protected], www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
