Importing existing data into Galaxy

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Importing existing data into Galaxy

Oren Livne
Dear All,

We have a large collection of large data files on our shared file
system. We would like to make a subset of them available to a galaxy
user session (based on user privileges; different subsets for different
users). We want to leave files in their original locations and point
galaxy to their paths without copying them.  What is the best option for
implementing this bridge? Remote data source/data library uploaded on
the fly/other?

Thanks,
Oren

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Re: [galaxy-dev] Importing existing data into Galaxy

Greg Von Kuster-2
Oren,

The best way to do this would be to use galaxy data libraries, uploading files from file system paths and not copying the files into the Galaxy file location.  

The following provides all of the details about data libraries:

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries


The following provides specific details about the various options for uploading files to data libraries.

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files

Let us know if you encounter any issues.

Greg Von Kuster


On Oct 27, 2011, at 4:31 PM, Oren Livne wrote:

> Dear All,
>
> We have a large collection of large data files on our shared file system. We would like to make a subset of them available to a galaxy user session (based on user privileges; different subsets for different users). We want to leave files in their original locations and point galaxy to their paths without copying them.  What is the best option for implementing this bridge? Remote data source/data library uploaded on the fly/other?
>
> Thanks,
> Oren
> ___________________________________________________________
> 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/

Greg Von Kuster
Galaxy Development Team
[hidden email]





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Re: [galaxy-dev] Importing existing data into Galaxy

Oren Livne
Dear Greg,

Thanks so much, this helps a lot. I created a public data library, but
it is not listed in the list of libraries on the left pane in "Analyze
Data". How can I access it and use its files in workflows?

Oren

On 10/27/2011 7:55 PM, Greg Von Kuster wrote:

> Oren,
>
> The best way to do this would be to use galaxy data libraries, uploading files from file system paths and not copying the files into the Galaxy file location.
>
> The following provides all of the details about data libraries:
>
> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries
>
>
> The following provides specific details about the various options for uploading files to data libraries.
>
> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
>
> Let us know if you encounter any issues.
>
> Greg Von Kuster
>
>
> On Oct 27, 2011, at 4:31 PM, Oren Livne wrote:
>
>> Dear All,
>>
>> We have a large collection of large data files on our shared file system. We would like to make a subset of them available to a galaxy user session (based on user privileges; different subsets for different users). We want to leave files in their original locations and point galaxy to their paths without copying them.  What is the best option for implementing this bridge? Remote data source/data library uploaded on the fly/other?
>>
>> Thanks,
>> Oren
>> ___________________________________________________________
>> 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/
> Greg Von Kuster
> Galaxy Development Team
> [hidden email]
>
>
>


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Re: [galaxy-dev] Importing existing data into Galaxy

Greg Von Kuster-2
Data libraries are accessible from the "Shared Data" pop-up menu in the top Galaxy menu bar.


On Oct 28, 2011, at 1:12 PM, Oren Livne wrote:

> Dear Greg,
>
> Thanks so much, this helps a lot. I created a public data library, but it is not listed in the list of libraries on the left pane in "Analyze Data". How can I access it and use its files in workflows?
>
> Oren
>
> On 10/27/2011 7:55 PM, Greg Von Kuster wrote:
>> Oren,
>>
>> The best way to do this would be to use galaxy data libraries, uploading files from file system paths and not copying the files into the Galaxy file location.
>>
>> The following provides all of the details about data libraries:
>>
>> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries
>>
>>
>> The following provides specific details about the various options for uploading files to data libraries.
>>
>> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
>>
>> Let us know if you encounter any issues.
>>
>> Greg Von Kuster
>>
>>
>> On Oct 27, 2011, at 4:31 PM, Oren Livne wrote:
>>
>>> Dear All,
>>>
>>> We have a large collection of large data files on our shared file system. We would like to make a subset of them available to a galaxy user session (based on user privileges; different subsets for different users). We want to leave files in their original locations and point galaxy to their paths without copying them.  What is the best option for implementing this bridge? Remote data source/data library uploaded on the fly/other?
>>>
>>> Thanks,
>>> Oren
>>> ___________________________________________________________
>>> 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/
>> Greg Von Kuster
>> Galaxy Development Team
>> [hidden email]
>>
>>
>>
>

Greg Von Kuster
Galaxy Development Team
[hidden email]





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(no subject)

Mahjoubeh Jalali
In reply to this post by Oren Livne

Dear All

How can I de-subscribe from the mailing list?
Any help would be appreciated

Kind Regards
M. J