Re: [galaxy-user] upload data to galaxy using terminal

2014-03-26 Thread Martin Čech
I don't understand your question. What is stopping your from using the API
from terminal?

However the easiest way to do it would probably be with Python and the
BioBlend project (http://bioblend.readthedocs.org/en/latest/ and
https://github.com/afgane/bioblend).

Another way is to set up a watcher in the folder that your tool is creating
files in and upload to Galaxy on change.

If none of these make sense to you please clarify your need.

thanks

Martin


On Wed, Mar 26, 2014 at 2:27 AM, do kadya  wrote:

> Thank you very much Martin Čech for reply.
> Currently I am uploading data by using linking method only,
> But what I wanted is NO API, that means via terminal only.
>
> As you can see my first mail where I am explaining query,
> MuSiC2 creating folders and files by itself, and hence galaxy will not be
> able to track those files.
> hence I want to collect those files and upload to current history (as data
> sets) using Terminal.
> Is that thing is possible ?
>
>  else how can I tell Galaxy that tool is creating folder first and then
> writing files ?
> I am usinghttp://cli-mate.lumc.nl/define#to create xml file for
> galaxy.
> I know I can hide output (from main command), but how can i track file
> which is inside folder ?
>
> Waiting for positive reply.
>
>
> On Tue, Mar 25, 2014 at 6:04 PM, Martin Čech  wrote:
>
>> Hi,
>>
>> yes, you can link files to a Galaxy Library without copying -  please see
>> https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles(the 
>> last part 'Upload files from filesystem paths').
>>
>> And there is an API for libraries (although it is under construction).
>> The flow of controllers for upload is api/library_contents >
>> controllers/library_common
>>
>>
>> https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.library_contents
>>
>> Martin
>>
>>
>> On Tue, Mar 25, 2014 at 7:47 AM, do kadya  wrote:
>>
>>> Hi,
>>> Can I upload data (mostly link the data) using terminal ?
>>>
>>> MuSiC 2 tool integration is not available in their website nor in tool
>>> shed.
>>> MuSiC 2 creates folder and files by itself, which is hard to track by
>>> Galaxy.
>>>
>>> So is there any way to link files to galaxy current work space so that I
>>> can link those distracted files which are created by MuSiC 2.
>>>
>>> ex: if you run
>>> music2   bmr calc-bmrfile_of_input
>>>
>>> output is 3 files,
>>> ./file1.txt
>>> ./folder1/file2.txt
>>> ./folder2/file3.txt
>>> we can not mention that we need this output filename or save file at
>>> specific location, we can not give this option.
>>>
>>>
>>> Galaxy will not able to track this output, hence i have to do it
>>> manually. So is it possible to upload this files manually by terminal ?
>>>
>>>
>>>
>>>
>>> Waiting for positive reply.
>>> Thank You
>>> - Chetan
>>>
>>> ___
>>> The Galaxy User list should be used for the discussion of
>>> Galaxy analysis and other features on the public server
>>> at usegalaxy.org.  Please keep all replies on the list by
>>> using "reply all" in your mail client.  For discussion of
>>> local Galaxy instances and the Galaxy source code, please
>>> use the Galaxy Development list:
>>>
>>>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>
>>> 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/
>>>
>>
>>
>
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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/

Re: [galaxy-user] upload data to galaxy using terminal

2014-03-25 Thread do kadya
Thank you very much Martin Čech for reply.
Currently I am uploading data by using linking method only,
But what I wanted is NO API, that means via terminal only.

As you can see my first mail where I am explaining query,
MuSiC2 creating folders and files by itself, and hence galaxy will not be
able to track those files.
hence I want to collect those files and upload to current history (as data
sets) using Terminal.
Is that thing is possible ?

else how can I tell Galaxy that tool is creating folder first and then
writing files ?
I am usinghttp://cli-mate.lumc.nl/define#to create xml file for
galaxy.
I know I can hide output (from main command), but how can i track file
which is inside folder ?

Waiting for positive reply.

On Tue, Mar 25, 2014 at 6:04 PM, Martin Čech  wrote:

> Hi,
>
> yes, you can link files to a Galaxy Library without copying -  please see
> https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles(the 
> last part 'Upload files from filesystem paths').
>
> And there is an API for libraries (although it is under construction). The
> flow of controllers for upload is api/library_contents >
> controllers/library_common
>
>
> https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.library_contents
>
> Martin
>
>
> On Tue, Mar 25, 2014 at 7:47 AM, do kadya  wrote:
>
>> Hi,
>> Can I upload data (mostly link the data) using terminal ?
>>
>> MuSiC 2 tool integration is not available in their website nor in tool
>> shed.
>> MuSiC 2 creates folder and files by itself, which is hard to track by
>> Galaxy.
>>
>> So is there any way to link files to galaxy current work space so that I
>> can link those distracted files which are created by MuSiC 2.
>>
>> ex: if you run
>> music2   bmr calc-bmrfile_of_input
>>
>> output is 3 files,
>> ./file1.txt
>> ./folder1/file2.txt
>> ./folder2/file3.txt
>> we can not mention that we need this output filename or save file at
>> specific location, we can not give this option.
>>
>>
>> Galaxy will not able to track this output, hence i have to do it
>> manually. So is it possible to upload this files manually by terminal ?
>>
>>
>>
>>
>> Waiting for positive reply.
>> Thank You
>> - Chetan
>>
>> ___
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>>
>>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>> 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/
>>
>
>
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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/

Re: [galaxy-user] upload data to galaxy using terminal

2014-03-25 Thread Martin Čech
Hi,

yes, you can link files to a Galaxy Library without copying -  please see
https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles(the
last part 'Upload files from filesystem paths').

And there is an API for libraries (although it is under construction). The
flow of controllers for upload is api/library_contents >
controllers/library_common

https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.library_contents

Martin


On Tue, Mar 25, 2014 at 7:47 AM, do kadya  wrote:

> Hi,
> Can I upload data (mostly link the data) using terminal ?
>
> MuSiC 2 tool integration is not available in their website nor in tool
> shed.
> MuSiC 2 creates folder and files by itself, which is hard to track by
> Galaxy.
>
> So is there any way to link files to galaxy current work space so that I
> can link those distracted files which are created by MuSiC 2.
>
> ex: if you run
> music2   bmr calc-bmrfile_of_input
>
> output is 3 files,
> ./file1.txt
> ./folder1/file2.txt
> ./folder2/file3.txt
> we can not mention that we need this output filename or save file at
> specific location, we can not give this option.
>
>
> Galaxy will not able to track this output, hence i have to do it manually.
> So is it possible to upload this files manually by terminal ?
>
>
>
>
> Waiting for positive reply.
> Thank You
> - Chetan
>
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> 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/
>
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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/