contributing patches to toolshed repos...

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contributing patches to toolshed repos...

Langhorst, Brad
What’s the right way to contribute additions to other people’s repos?

I have extended the picard wrappers to support the rna-seq metrics and downsample sam tools, but I don’t want to start a new repo just for these.


I have attached  the output from hg outgoing -p in case that’s useful

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picard_updates.patch (21K) Download Attachment
ATT00001.htm (1K) Download Attachment
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Re: contributing patches to toolshed repos...

Björn Grüning-3
Hi Brad,

unfortunately there is no standard way to contribute back to the
repositories. Many of us have a github/bitbucket repositories with the
wrappers.

There are a few tickets to make that best practise, for example:
https://trello.com/c/WdShmMld

For the time being, please create a trello card at:

https://trello.com/b/vHqpKpZF/galaxy-tool-shed

and attach your patch. If you can't attach it, I will do it for you.

Thanks a lot for your contribution!
Bjoern

> What’s the right way to contribute additions to other people’s repos?
>
> I have extended the picard wrappers to support the rna-seq metrics and downsample sam tools, but I don’t want to start a new repo just for these.
>
>
> I have attached  the output from hg outgoing -p in case that’s useful
>
>
>
> ___________________________________________________________
> 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:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>

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Re: contributing patches to toolshed repos...

Peter Cock
On Tue, Feb 25, 2014 at 4:53 PM, Björn Grüning
<[hidden email]> wrote:

> Hi Brad,
>
> unfortunately there is no standard way to contribute back to the
> repositories. Many of us have a github/bitbucket repositories with the
> wrappers.
>
> There are a few tickets to make that best practise, for example:
> https://trello.com/c/WdShmMld
>
> For the time being, please create a trello card at:
>
> https://trello.com/b/vHqpKpZF/galaxy-tool-shed
>
> and attach your patch. If you can't attach it, I will do it for you.
>
> Thanks a lot for your contribution!
> Bjoern

I presume in this case the tools were from the Galaxy core team
(and originally in Galaxy itself)?

For the other case of community developed tools, each repository
README file should link to a home page or repository - for example
Bjoern and I both use GitHub for our tools. There is a Trello card
open about making this more explicit on the Tool Shed:

https://trello.com/c/g1dt8WhA/57-tool-shed-should-include-url-field-s-for-homepage-github-or-bitbucket-repository-issue-bug-tracker

Peter

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Re: contributing patches to toolshed repos...

Langhorst, Brad
In reply to this post by Björn Grüning-3
Hi Bjorn:

I don’t appear to have permission to create cards on the the galaxy-tool-shed board…

I can create cards on the main board via http://galaxyproject.org/trello
but I can’t find an analog for the toolshed board.

Am I missing something?


Brad
--
Brad Langhorst, Ph.D.
Applications and Product Development Scientist

On Feb 25, 2014, at 11:53 AM, Björn Grüning <[hidden email]> wrote:

> Hi Brad,
>
> unfortunately there is no standard way to contribute back to the repositories. Many of us have a github/bitbucket repositories with the wrappers.
>
> There are a few tickets to make that best practise, for example:
> https://trello.com/c/WdShmMld
>
> For the time being, please create a trello card at:
>
> https://trello.com/b/vHqpKpZF/galaxy-tool-shed
>
> and attach your patch. If you can't attach it, I will do it for you.
>
> Thanks a lot for your contribution!
> Bjoern
>
>> What’s the right way to contribute additions to other people’s repos?
>>
>> I have extended the picard wrappers to support the rna-seq metrics and downsample sam tools, but I don’t want to start a new repo just for these.
>>
>>
>> I have attached  the output from hg outgoing -p in case that’s useful
>>
>>
>>
>> ___________________________________________________________
>> 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:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>


___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: contributing patches to toolshed repos...

Björn Grüning-3
Hi Brad,

interesting. I have CC'ed Greg, maybe he can get help us.
In the meantime, please create it under the Galaxy ToolShed. It's
probably not really defined in which board we should create Tool issues.

Thanks!
Bjoern

> Hi Bjorn:
>
> I don’t appear to have permission to create cards on the the galaxy-tool-shed board…
>
> I can create cards on the main board via http://galaxyproject.org/trello
> but I can’t find an analog for the toolshed board.
>
> Am I missing something?
>
>
> Brad
> --
> Brad Langhorst, Ph.D.
> Applications and Product Development Scientist
>
> On Feb 25, 2014, at 11:53 AM, Björn Grüning <[hidden email]> wrote:
>
>> Hi Brad,
>>
>> unfortunately there is no standard way to contribute back to the repositories. Many of us have a github/bitbucket repositories with the wrappers.
>>
>> There are a few tickets to make that best practise, for example:
>> https://trello.com/c/WdShmMld
>>
>> For the time being, please create a trello card at:
>>
>> https://trello.com/b/vHqpKpZF/galaxy-tool-shed
>>
>> and attach your patch. If you can't attach it, I will do it for you.
>>
>> Thanks a lot for your contribution!
>> Bjoern
>>
>>> What’s the right way to contribute additions to other people’s repos?
>>>
>>> I have extended the picard wrappers to support the rna-seq metrics and downsample sam tools, but I don’t want to start a new repo just for these.
>>>
>>>
>>> I have attached  the output from hg outgoing -p in case that’s useful
>>>
>>>
>>>
>>> ___________________________________________________________
>>> 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:
>>>    http://lists.bx.psu.edu/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>    http://galaxyproject.org/search/mailinglists/
>>>
>>
>

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Re: contributing patches to toolshed repos...

Greg Von Kuster
Hi Brad and Björn,

Tickets can currently only be added to the Galaxy Trello Board, so please add them there and we'll move them to the Tool Shed Trello board whenever appropriate.  Hopefully we'll soon have the ability for tickets to be submitted to multiple boards.

Thanks very much!

Greg Von Kuster


On Feb 25, 2014, at 3:34 PM, Björn Grüning <[hidden email]> wrote:

> Hi Brad,
>
> interesting. I have CC'ed Greg, maybe he can get help us.
> In the meantime, please create it under the Galaxy ToolShed. It's probably not really defined in which board we should create Tool issues.
>
> Thanks!
> Bjoern
>
>> Hi Bjorn:
>>
>> I don’t appear to have permission to create cards on the the galaxy-tool-shed board…
>>
>> I can create cards on the main board via http://galaxyproject.org/trello
>> but I can’t find an analog for the toolshed board.
>>
>> Am I missing something?
>>
>>
>> Brad
>> --
>> Brad Langhorst, Ph.D.
>> Applications and Product Development Scientist
>>
>> On Feb 25, 2014, at 11:53 AM, Björn Grüning <[hidden email]> wrote:
>>
>>> Hi Brad,
>>>
>>> unfortunately there is no standard way to contribute back to the repositories. Many of us have a github/bitbucket repositories with the wrappers.
>>>
>>> There are a few tickets to make that best practise, for example:
>>> https://trello.com/c/WdShmMld
>>>
>>> For the time being, please create a trello card at:
>>>
>>> https://trello.com/b/vHqpKpZF/galaxy-tool-shed
>>>
>>> and attach your patch. If you can't attach it, I will do it for you.
>>>
>>> Thanks a lot for your contribution!
>>> Bjoern
>>>
>>>> What’s the right way to contribute additions to other people’s repos?
>>>>
>>>> I have extended the picard wrappers to support the rna-seq metrics and downsample sam tools, but I don’t want to start a new repo just for these.
>>>>
>>>>
>>>> I have attached  the output from hg outgoing -p in case that’s useful
>>>>
>>>>
>>>>
>>>> ___________________________________________________________
>>>> 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:
>>>>   http://lists.bx.psu.edu/
>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>>   http://galaxyproject.org/search/mailinglists/
>>>>
>>>
>>
>
> ___________________________________________________________
> 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:
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
>


___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
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