tool publishing

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tool publishing

Matthias Bernt
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,
[hidden email], 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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Re: tool publishing

Peter Briggs
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 [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482


________________________________________
From: galaxy-dev [[hidden email]] on behalf of Matthias Bernt [[hidden email]]
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,
[hidden email], 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/
___________________________________________________________
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:
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Re: tool publishing

Matthias Bernt
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 [hidden email]
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
>
> ________________________________________
> From: galaxy-dev [[hidden email]] on behalf of Matthias Bernt [[hidden email]]
> 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,
> [hidden email], 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,
[hidden email], 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/
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Re: tool publishing

Marius van den Beek
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 <[hidden email]> 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 [hidden email]
>> Bioinformatics Core Facility University of Manchester
>> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>>
>>
>> ________________________________________
>> From: galaxy-dev [[hidden email]] on behalf of
>> Matthias Bernt [[hidden email]]
>> 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,
>> [hidden email], 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,
> [hidden email], 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/
___________________________________________________________
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/
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Re: tool publishing

Matthias Bernt
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 <[hidden email]> 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 [hidden email]
>>> Bioinformatics Core Facility University of Manchester
>>> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>>>
>>>
>>> ________________________________________
>>> From: galaxy-dev [[hidden email]] on behalf of
>>> Matthias Bernt [[hidden email]]
>>> 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,
>>> [hidden email], 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,
>> [hidden email], 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,
[hidden email], 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/
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Re: tool publishing

Marius van den Beek
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 <[hidden email]> 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 <[hidden email]> 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 [hidden email]
>>>> Bioinformatics Core Facility University of Manchester
>>>> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>>>>
>>>>
>>>> ________________________________________
>>>> From: galaxy-dev [[hidden email]] on behalf
>>>> of
>>>> Matthias Bernt [[hidden email]]
>>>> 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,
>>>> [hidden email], 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,
>>> [hidden email], 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,
> [hidden email], 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:
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