Library Usage Screencast?

9.4 years ago by

Penn State

Erick: There are currently no screencasts detailing libraries, but this is one of the priorities for future screencasts. We will have an initial set made by mid-August. anton galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://galaxyproject.org

ADD COMMENT • link written 9.4 years ago by Anton Nekrutenko ♦ 1.7k

Erick, In the meantime, to answer your question about config settings for the dataset security and library stuff, the following 4 settings can be be used: # Admin Users # This should be a comma-separated list of valid Galaxy users - this # will eventually be replaced with users associated with an 'admin' group # admin_users = ... # Can admin users register new accounts? # allow_user_creation = True # Can an admin user delete user accounts? # allow_user_deletion = True # Directories of files contained in the following directory can be uploaded to a library from the Admin view #library_import_dir = /var/opt/galaxy/import # The following can be configured to allow non-admin users to upload a directory of files. The # configured directory must contain sub-directories named the same as the non-admin user's Galaxy # login ( email ). The non-admin user is restricted to uploading files or sub-directories of files # contained in their directory. # user_library_import_dir = /var/opt/galaxy/import/users

ADD REPLY • link written 9.4 years ago by Greg Von Kuster • 840

Greg, I managed to create and share some libraries. However, it was not that clear to me how the library_import_dir and user_library_import_dir should be used and what do they mean to the user interacting through the web interface.... Could you please comment a bit on it? thanks, Erick 2009/7/15 Greg Von Kuster <ghv2@psu.edu>

ADD REPLY • link written 9.4 years ago by Erick Antezana • 570

Erick, The current use for these config settings is fairly limited, and sort of a stop-gap measure ( fairly weak, but somewhat useful ) until we provide a more ideal solution ( currently in progress ). The "library_import_dir" setting is for an admin user only, and it can point to a directory on the Galaxy server where files can be placed for uploading into a library. It allows for uploading a complete directory of files instead of 1 file at a time ( or a sub-directory within the directory pointed to by the config setting ). The "user_library_import_dir"setting is for non-admin users that have files ( e.g., a set of sequence runs ) that they want to upload to a library. The Galaxy admin should create subdirectories within this directory ( pointed to by the config setting ) that are named the same as the non-admin user's Galaxy account ( email ). The non-admin users can then ftp their files into their specified directory, and upload the directory of files into a library ( assuming the Galaxy admin has given them the "library add" privilege on the folder to which they are uploading ). Greg

ADD REPLY • link written 9.4 years ago by Greg Von Kuster • 840

Greg, thanks for the explanation. I manage to upload a couple of huge datasets, etc. However, I faced an issue while trying to give access ("Role members can import this dataset into their history for analysis") to more than one user, I get the following error message: At least 1 user must have every role associated with accessing dataset 'seq4588.fastq'. The roles you attempted to associate for access would make this dataset inaccessible by everyone, so access permissions were not set. All other permissions were updated for the dataset. any suggestion? Am I missing something? On the other hand, would it be possible to add/implement a button that facilitates the browsing over the libraries, datases, folders, etc by collapsing or expanding the tree in ONE click? Otherwise, users have to click many times on the small triangles to arrive to his/her dataset that is buried 10 levels deep in the tree... thanks, Erick 2009/7/16 Greg Von Kuster <ghv2@psu.edu>

ADD REPLY • link written 9.4 years ago by Erick Antezana • 570

Hi Erick, You are probably attempting to set 2 different private roles with the access permission on the dataset. Instead, create a role, with whatever users you want to share the data, and associate that role with the access privilege on the dataset. I just completed a long interaction with another user on this ( in the galaxy-user mail list ), so I'll add the content here for your benefit. 2) access: Role members can import this dataset into their history for All roles are required because of the complication of derived permissions for datasets that are produced from running jobs on different input datasets. Take, for example, two datasets, DatasetA, and DatasetB. Access to DatasetA requires a user to be associated with RoleA, and access to DatasetB with RoleB. It follows that DatasetAB ( created by running a tool with DatasetA and DatasetB as inputs ) should have both RoleA and RoleB associated for the access permission. However, if ANY associated role was sufficient, this would allow users who are only associated either RoleA OR RoleB to view data which was originally not accessible to them. We'll take this under consideration.

ADD REPLY • link written 9.4 years ago by Greg Von Kuster • 840

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