Re: [galaxy-dev] Toolshed Question, In reference to https://toolshed.g2.bx.psu.edu/view/youngkim/ezbamqc/caed0168f704

[Peter Cock]

On Wed, Mar 30, 2016 at 9:46 PM, Molik, David  wrote:
> We're uploading a tool to the Galaxy Toolshed and were wondering about sample 
> files:
>
> Should .loc.sample files refer to sample data ( test-data )
> or should they be generalized for integration into other instances of Galaxy?

Any sample loc files should be provided named tool-data/example.loc.sample
and will be copied as example.loc to give default values for the system. This
may just mean a section of comment lines with no actual values, or perhaps
you can give useful defaults?

Here's an example where useful defaults made sense - and these are
also used in the tool's functional tests:

https://github.com/peterjc/pico_galaxy/blob/master/tool-data/effectiveT3.loc.sample
https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3

If you want to write functional tests using test entries in the example.loc file
(i.e. entries not in the default values provided in your
example.loc.sample file),
use tests-data/example.loc instead and the special value ${__HERE__} to
take case of giving a full path.

e.g. sample file with no real entries:
https://github.com/peterjc/galaxy_blast/tree/master/tool-data/blastdb_p.loc.sample
vs. test file pointing at some test entries:
https://github.com/peterjc/galaxy_blast/tree/master/test-data/blastdb_p.loc

I'm not sure if this last part has made it into the official
documentation yet...

> Also, how should dependencies be noted?
>

Can you be a bit more precise?

Probably the answer is tool_dependencies.xml etc, e.g.
https://wiki.galaxyproject.org/ToolsWithDependenciesInSeparateRepositories

Peter
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[galaxy-dev] file transference between different galaxy servers...

[Danilo Ceschin]

hi,
I have some big files uploaded at
galaxy.ncgas-trinity.indiana.edu
and I would like to use those file at
https://usegalaxy.org/
Is there a way to transfer those files to avoid upload them again? My 
internet connection is very bad and it takes days just for one file.

Thank in advance.
sincerely yours,

--
Danilo Ceschin PhD
Fac. de Ciencias Agrarias
IBAC - Instituto de Biotecnología Agropecuaria del Comahue
Ruta 151 - Km 12,5
CP 8303 - Cinco Saltos - Río Negro
Argentina

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Re: [galaxy-dev] file transference between different galaxy servers...

[Jennifer Hillman-Jackson]

Opps, that should be "control-click" on a MAC OSX - sorry!

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Wed, Mar 30, 2016 at 10:10 AM, Jennifer Hillman-Jackson <
j...@galaxyproject.org> wrote:

> Hi Danilo,
>
> 1. Copy the URL for the dataset: option+click on the disc icon and choose
> "Copy Link Address"
> 2. Paste the URL into the Upload tool form: Paste/Fetch data
>
> Many can be done at once. Copy/paste the URLs into a temporary text file
> first, one per line, then copy/paste into the upload form.
>
> Thanks!
>
> Jen
>
> --
> Jennifer Hillman-Jackson
> Galaxy Application Support
> http://usegalaxy.org
> http://galaxyproject.org
> http://biostar.usegalaxy.org
>
>
> On Wed, Mar 30, 2016 at 4:38 AM, Danilo Ceschin 
> wrote:
>
>> hi,
>> I have some big files uploaded at
>> galaxy.ncgas-trinity.indiana.edu
>> and I would like to use those file at
>> https://usegalaxy.org/
>> Is there a way to transfer those files to avoid upload them again? My
>> internet connection is very bad and it takes days just for one file.
>> Thank in advance.
>> sincerely yours,
>>
>> --
>> Danilo Ceschin PhD
>> Fac. de Ciencias Agrarias
>> IBAC - Instituto de Biotecnología Agropecuaria del Comahue
>> Ruta 151 - Km 12,5
>> CP 8303 - Cinco Saltos - Río Negro
>> Argentina
>>
>> ___
>> 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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