Hi Matthias, this really looks like it should have worked. The repository has been created, but the revision is not installable. Often times this is because of missing tool data table / loc file references, but I see that your tool is not making use of any of these so they are not necessary. My typical command line invocation contains the API key, like so: ``` planemo shed_update -t testtoolshed --shed_key $MY_KEY ``` Perhaps something is going wrong when passing the credentials around in planemo, so that only the repo creation phase succeeds. Maybe you'd have more luck explicitly passing in the repo key ? 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. Marius On 18 December 2017 at 10:49, Matthias Bernt <m.bernt@ufz.de> 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 peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

________________________________________ From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of Matthias Bernt [m.bernt@ufz.de] 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, m.bernt@ufz.de, 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/

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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, m.bernt@ufz.de, 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/

Hi Matthias, Glad it works. I guess a few characters are blacklisted, but generally you can choose freely. You can see your public name (which is what should be used in the `name` field) by logging in to the toolshed, User -> Preferences -> Manage your Information. Marius On 18 December 2017 at 11:20, Matthias Bernt <m.bernt@ufz.de> wrote:

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 <m.bernt@ufz.de> 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 peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

________________________________________ From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of Matthias Bernt [m.bernt@ufz.de] 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, m.bernt@ufz.de, 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, m.bernt@ufz.de, 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, m.bernt@ufz.de, 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 -------------------------------------------