Galaxy Data Libraries - Revision history

Mvccouto@uab.edu: /* Setting permissions on a sub-directory */

2013-06-19T19:20:06Z

Setting permissions on a sub-directory

← Older revision		Revision as of 19:20, 19 June 2013
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	==== Setting permissions on a sub-directory ====		==== Setting permissions on a sub-directory ====
	Galaxy application needs recursive read and browse permissions on a subdirectory that will be copied or linked. This can be done using following Access Control List (ACL) command:		Galaxy application needs recursive read and browse permissions on a subdirectory that will be copied or linked. This can be done using following Access Control List (ACL) command:
	setfacl -R -m u:galaxy:rx /~~lustre~~/~~scratch~~/$USER/demo-datasets		setfacl -R -m u:galaxy:rx /scratch/user/$USER/demo-datasets

	After setting appropriate read permissions for Galaxy application, the directory can be imported by selecting it in the drop-down menu and copying or linking it to the Galaxy.		After setting appropriate read permissions for Galaxy application, the directory can be imported by selecting it in the drop-down menu and copying or linking it to the Galaxy.
	[[File:Uploading_Dir_Of_Files_Data_Lib.png\|730px]]		[[File:Uploading_Dir_Of_Files_Data_Lib.png\|730px]]

Pavgi@uab.edu: /* Setting permissions on a sub-directory */

2013-03-08T16:39:07Z

Setting permissions on a sub-directory

← Older revision		Revision as of 16:39, 8 March 2013
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	After setting appropriate read permissions for Galaxy application, the directory can be imported by selecting it in the drop-down menu and copying or linking it to the Galaxy.		After setting appropriate read permissions for Galaxy application, the directory can be imported by selecting it in the drop-down menu and copying or linking it to the Galaxy.
	[[File:Uploading_Dir_Of_Files_Data_Lib.png]]		[[File:Uploading_Dir_Of_Files_Data_Lib.png\|730px]]

Pavgi@uab.edu: /* Setting permissions on a sub-directory */

2013-03-08T16:38:33Z

Setting permissions on a sub-directory

← Older revision		Revision as of 16:38, 8 March 2013
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	After setting appropriate read permissions for Galaxy application, the directory can be imported by selecting it in the drop-down menu and copying or linking it to the Galaxy.		After setting appropriate read permissions for Galaxy application, the directory can be imported by selecting it in the drop-down menu and copying or linking it to the Galaxy.
	[[File:Uploading_Dir_Of_Files_Data_Lib]]		[[File:Uploading_Dir_Of_Files_Data_Lib.png]]

Pavgi@uab.edu at 16:38, 8 March 2013

2013-03-08T16:38:15Z

← Older revision		Revision as of 16:38, 8 March 2013
Line 30:		Line 30:

	After setting appropriate read permissions for Galaxy application, the directory can be imported by selecting it in the drop-down menu and copying or linking it to the Galaxy.		After setting appropriate read permissions for Galaxy application, the directory can be imported by selecting it in the drop-down menu and copying or linking it to the Galaxy.
			[[File:Uploading_Dir_Of_Files_Data_Lib]]

Pavgi@uab.edu: updated image pixel size

2013-03-08T16:34:10Z

updated image pixel size

← Older revision		Revision as of 16:34, 8 March 2013
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	== Accessing a data library ==		== Accessing a data library ==
	A data library can be accessed by clicking 'Shared Data --> Data Libraries' item in the top menu bar.		A data library can be accessed by clicking 'Shared Data --> Data Libraries' item in the top menu bar.
	[[File:Accessing_Data_Lib.png]]		[[File:Accessing_Data_Lib.png\|730px]]

	== Adding datasets to the data library ==		== Adding datasets to the data library ==
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	=== Upload files ===		=== Upload files ===
	The first option allows uploading files using a web browser and pasting external URL locations.		The first option allows uploading files using a web browser and pasting external URL locations.
	[[File:Uploading_Files_Data_Lib.png]]		[[File:Uploading_Files_Data_Lib.png\|730px]]

	=== Upload directory of files ===		=== Upload directory of files ===

Pavgi@uab.edu: /* Creating a new data library */

2013-03-08T16:33:30Z

Creating a new data library

← Older revision		Revision as of 16:33, 8 March 2013
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	== Creating a new data library ==		== Creating a new data library ==
	Right now Galaxy supports data library creation only for administrative users. You can request a new data library by sending an email to [mailto:galaxy-help@vo.uabgrid.uab.edu UAB Galaxy help list]. Please mention name, description and synopsis (optional) for your new data library. You will have full permissions to manage your data library access.		Right now Galaxy supports data library creation only for administrative users. You can request a new data library by sending an email to [mailto:galaxy-help@vo.uabgrid.uab.edu UAB Galaxy help list]. Please mention name, description and synopsis (optional) for your new data library. You will have full permissions to manage your data library access.
	[[File:Managing_Data_Lib.png]]		[[File:Managing_Data_Lib.png\|730px]]

	== Accessing a data library ==		== Accessing a data library ==

Pavgi@uab.edu: initial draft for data library uploads

2013-03-08T16:27:44Z

initial draft for data library uploads

New page

Galaxy has a concept of 'Data Libraries' which is a data container to organize files in an hierarchical manner, similar to directories on a desktop. Data libraries provide other features for data organization and sharing as well. You can add datasets to a data library by uploading them through a web browser, pasting external URL paths or referencing existing directory in $USER_SCRATCH on Cheaha.

== Creating a new data library ==
Right now Galaxy supports data library creation only for administrative users. You can request a new data library by sending an email to [mailto:galaxy-help@vo.uabgrid.uab.edu UAB Galaxy help list]. Please mention name, description and synopsis (optional) for your new data library. You will have full permissions to manage your data library access.
[[File:Managing_Data_Lib.png]]

== Accessing a data library ==
A data library can be accessed by clicking 'Shared Data --> Data Libraries' item in the top menu bar.
[[File:Accessing_Data_Lib.png]]

== Adding datasets to the data library ==
Data library provides three options to add datasets:
* Upload files
* Upload directory of files
* Import datasets in your current history

=== Upload files ===
The first option allows uploading files using a web browser and pasting external URL locations.
[[File:Uploading_Files_Data_Lib.png]]

=== Upload directory of files ===
The second option lists existing directories in $USER_SCRATCH on Cheaha. Click on 'Server directory' drop-down menu to
see a list of files in your $USER_SCRATCH. Galaxy application needs read and browse permissions to use this upload option.
==== Setting permissions on $USER_SCRATCH ====
Galaxy application needs read and browse permissions on the $USER_SCRATCH and they can be set using Access Control List (ACL):
setfacl -m u:galaxy:rx /scratch/user/$USER
==== Setting permissions on a sub-directory ====
Galaxy application needs recursive read and browse permissions on a subdirectory that will be copied or linked. This can be done using following Access Control List (ACL) command:
setfacl -R -m u:galaxy:rx /lustre/scratch/$USER/demo-datasets

After setting appropriate read permissions for Galaxy application, the directory can be imported by selecting it in the drop-down menu and copying or linking it to the Galaxy.