Re: [galaxy-dev] planemo shed_create bug? on planemo/server docker image

[Björn Grüning]

Am 14.07.2016 um 09:33 schrieb Steve Cassidy:
> Hi Bjorn, thanks for the response, very happy to go with the future
> way of doing things.  I did see the references to conda but couldn’t
> quite decipher what was needed.
> 
> Are you saying that I should create a new recipe in bioconda for my
> dependency? 

Yes :)

> Does it matter that this is not in the least ‘bio’ -
> these are for our language analysis tools, in the first instance this
> is a tool to pull data from our language repository.

No this does not matter, just put it in :)

> How does Galaxy know about the bioconda channel - is there a
> configuration setting pointing to the channels to find dependencies
> in?

Yes, please look in your galaxy.ini and search for conda.

> Could we create a language-conda channel to house language
> dependencies? Does that question make sense (not totally up on conda
> yet).

Yes this question makes sense, but than you have this additional
overhead of maintaining the build-infrastructure, building a community
around it, merging PR ... and so on.
From my experience this is quite a bit of work!

Cheers,
Bjoern

> Steve
> 
> — Department of Computing, Macquarie University 
> http://web.science.mq.edu.au/~cassidy
> 
>> On 14 Jul 2016, at 5:00 PM, Björn Grüning
>>  wrote:
>> 
>> Hi Steve,
>> 
>> are you fine restricting your tools to a recent Galaxy version,
>> let's say 6 month old?
>> 
>> If you forget about tool_depenencies.xml files, completely forget
>> these! Conda packaging is the way to go and way more easy for you.
>> 
>> Let me know and I will give a short introduction or follow the 
>> description on https://github.com/bioconda/bioconda-recipes to
>> create a PR and a package for your tool.
>> 
>> This can be used by Galaxy automatically. Thanks, Bjoern
>> 
>> Am 14.07.2016 um 03:49 schrieb Steve Cassidy:
>>> I’m just getting my head around tool dependencies and in doing so
>>> trying to push my tools to a local toolshed which I can handily
>>> run with the planemo/server docker image via Kitematic.
>>> 
>>> That toolshed is set up with an admin user
>>> plan...@test.com so I have a stanza in
>>> my .planemo.yml:
>>> 
>>> shed_username: "stevecassidy" sheds: http://localhost:32768/: 
>>> key: "" email: "plan...@test.com" 
>>> password: "planemo"
>>> 
>>> Now I try to create a repository in the toolshed with planemo:
>>> 
>>> $ planemo shed_create --shed_target http://localhost:32768/ 
>>> Repository created cd
>>> '/Users/steve/projects/hcsvlab-galaxy/tools/alveo' && git
>>> rev-parse HEAD cd
>>> '/Users/steve/projects/hcsvlab-galaxy/tools/alveo' && git diff
>>> --quiet Repository [alveoimport] does not exist in the targeted
>>> Tool Shed.
>>> 
>>> 
>>> Note the conflicting messages here. The repository is created
>>> (and I can confirm that it is there) but then I get the message
>>> that the repo does not exist in the Toolshed.  After a bit of
>>> digging it turns out that this is because the repo is owned by
>>> the user ‘planemo’ rather than my username as declared in
>>> .planemo.yml.  If I add —owner plane to the command then it works
>>> fine.
>>> 
>>> So I’m not sure if this is a bug in the shed_create code or a
>>> weird interaction with the setup on planemo/server.
>>> 
>>> Steve
>>> 
>>> — Department of Computing, Macquarie University 
>>> http://web.science.mq.edu.au/~cassidy
>>> 
>>> 
>>> 
>>> ___ 
>>> 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/mailinglists/
> 
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Re: [galaxy-dev] planemo shed_create bug? on planemo/server docker image

[Steve Cassidy]

Hi Bjorn,
  thanks for the response, very happy to go with the future way of doing 
things.  I did see the references to conda but couldn’t quite decipher what was 
needed. 

Are you saying that I should create a new recipe in bioconda for my dependency? 
Does it matter that this is not in the least ‘bio’ - these are for our language 
analysis tools, in the first instance this is a tool to pull data from our 
language repository.  

How does Galaxy know about the bioconda channel - is there a configuration 
setting pointing to the channels to find dependencies in? Could we create a 
language-conda channel to house language dependencies? Does that question make 
sense (not totally up on conda yet).

Steve 

—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

> On 14 Jul 2016, at 5:00 PM, Björn Grüning  wrote:
> 
> Hi Steve,
> 
> are you fine restricting your tools to a recent Galaxy version, let's
> say 6 month old?
> 
> If you forget about tool_depenencies.xml files, completely forget these!
> Conda packaging is the way to go and way more easy for you.
> 
> Let me know and I will give a short introduction or follow the
> description on https://github.com/bioconda/bioconda-recipes to create a
> PR and a package for your tool.
> 
> This can be used by Galaxy automatically.
> Thanks,
> Bjoern
> 
> Am 14.07.2016 um 03:49 schrieb Steve Cassidy:
>> I’m just getting my head around tool dependencies and in doing so trying to 
>> push my tools to a local toolshed which I can handily run with the 
>> planemo/server docker image via Kitematic.
>> 
>> That toolshed is set up with an admin user 
>> plan...@test.com so I have a stanza in my 
>> .planemo.yml:
>> 
>> shed_username: "stevecassidy"
>> sheds:
>>  http://localhost:32768/:
>>key: ""
>>email: "plan...@test.com"
>>password: "planemo"
>> 
>> Now I try to create a repository in the toolshed with planemo:
>> 
>> $ planemo shed_create --shed_target http://localhost:32768/
>> Repository created
>> cd '/Users/steve/projects/hcsvlab-galaxy/tools/alveo' && git rev-parse HEAD
>> cd '/Users/steve/projects/hcsvlab-galaxy/tools/alveo' && git diff --quiet
>> Repository [alveoimport] does not exist in the targeted Tool Shed.
>> 
>> 
>> Note the conflicting messages here. The repository is created (and I can 
>> confirm that it is there) but then I get the message that the repo does not 
>> exist in the Toolshed.  After a bit of digging it turns out that this is 
>> because the repo is owned by the user ‘planemo’ rather than my username as 
>> declared in .planemo.yml.  If I add —owner plane to the command then it 
>> works fine.
>> 
>> So I’m not sure if this is a bug in the shed_create code or a weird 
>> interaction with the setup on planemo/server.
>> 
>> Steve
>> 
>> —
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy
>> 
>> 
>> 
>> ___
>> 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/mailinglists/

___
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[galaxy-dev] planemo shed_create bug? on planemo/server docker image

[Steve Cassidy]

I’m just getting my head around tool dependencies and in doing so trying to 
push my tools to a local toolshed which I can handily run with the 
planemo/server docker image via Kitematic.

That toolshed is set up with an admin user 
plan...@test.com so I have a stanza in my .planemo.yml:

shed_username: "stevecassidy"
sheds:
  http://localhost:32768/:
key: ""
email: "plan...@test.com"
password: "planemo"

Now I try to create a repository in the toolshed with planemo:

$ planemo shed_create --shed_target http://localhost:32768/
Repository created
cd '/Users/steve/projects/hcsvlab-galaxy/tools/alveo' && git rev-parse HEAD
cd '/Users/steve/projects/hcsvlab-galaxy/tools/alveo' && git diff --quiet
Repository [alveoimport] does not exist in the targeted Tool Shed.


Note the conflicting messages here. The repository is created (and I can 
confirm that it is there) but then I get the message that the repo does not 
exist in the Toolshed.  After a bit of digging it turns out that this is 
because the repo is owned by the user ‘planemo’ rather than my username as 
declared in .planemo.yml.  If I add —owner plane to the command then it works 
fine.

So I’m not sure if this is a bug in the shed_create code or a weird interaction 
with the setup on planemo/server.

Steve

—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

___
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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  http://galaxyproject.org/search/mailinglists/