GALAXY input/output directory

Question: GALAXY input/output directory

3.7 years ago by

Switzerland

k.mamoud • 30 wrote:

Hello everyone,

I have quetions about the input and output directories of Galaxy.

For input I can can change it from the galaxy.ini file and create for each user an unique directory then they can import their data into Galaxy. But the question is can we have different directories for one user.

Second question is concerning the output, files of all the users jobs is written in /files. But can I tell to Galaxy to put for a specific job the output files not into files/ but in a specific folder without using copy or move.

Thanks for your help in advance,

import galaxy shared_data export • 2.0k views

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modified 3.6 years ago • written 3.7 years ago by k.mamoud • 30

3.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

As far as I know, there is only one location for inputs and one destination for outputs permitted. The clone or copy function can be used within the Galaxy UI to duplicate data (these are just links to the original).

That said, if running your own, you could set up some system to clones output data to another location then delete it in the Galaxy file system. DO NOT just move it, this would probably cause problems. Clone to put the copy where you want it, then go back and remove it from Galaxy. This could all be done through a script and API calls to Galaxy.

For inputs, you could set up a library for each user and then they use data from there. There are a few ways to load data into libraries, including directly from the file system (either loaded or just a link). Permissions could be set to restrict access. An administrator would need to load the library data, but this again could be scripted out. Help for Data Libraries admin data loading is here:
http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles

For more about libraries and related functions, have a look at the "Admin" hub. Most topics are covered in some level of details, many with complete tutorials.
http://wiki.galaxyproject.org/Admin

If others from our team or community wish to post more advice or methods implemented on locals, please feel free to add more on this thread!

Best, Jen, Galaxy team

ADD COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k

3.7 years ago by

k.mamoud • 30

Switzerland

k.mamoud • 30 wrote:

Hello,

thanks Jennifer for you answer,

I wanted to know if it possible with the get data tool, to upload data not in the current computer but link the path to mount directories which are in a server ?

Thanks in advance,

Best

ADD COMMENT • link modified 3.7 years ago • written 3.7 years ago by k.mamoud • 30

If the data on the other servers is hosted publically, then the URL method of upload through the upload tool would be possible. These can be user/password protected - just include that information in the URL (with special characters like "@" converted to hex).

ADD REPLY • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

ps: next time for new questions, it is best to start a new post. this helps keep each post focused on a single topic and also gets everyone's attention on "new" posts. You can always reference prior posts by URL if that helps to clarify your new question. Thanks!

ADD REPLY • link modified 3.6 years ago • written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

3.6 years ago by

k.mamoud • 30

Switzerland

k.mamoud • 30 wrote:

Dear all,

I am coming back on the input files subject.

To upload heavy data to the Galaxy histories I am using the data libraries API.

But it is limited because I can do it by creating a library for each user that is the user name (email).

But when you are admin you can upload directly by using the option "upload files from filessystem paths" .

I was wondering if it is not possible or if someone add this option to the shared data api for any user (non-admin).

Thanks in advance,

ADD COMMENT • link written 3.6 years ago by k.mamoud • 30

As far as I know, loading data into libraries is always a function restricted to accounts with "admin" status. Through whatever method explained in the first link I sent you (upload to data libs). This is not a planned function to be included in the interface upload tool or API for general users.

That said, there are a few ways around this.

1. grant admin permissions to your users, or some set of users, for them to manage the data

2. have users upload large data (by FTP or URL) into their accounts, then notify you which data to put into a library to share it with others

3. develop a "dropbox" type of system where users stage data on a file system convenient to all. Then, you as admin run scripts to do the loading into libraries, setting of permissions, and the like. much could be automated (a cron could search for data at regular intervals, etc.)

There could be other methods used by admins to do similar tasks of course. This may be a question worth asking on the galaxy-dev A.T galaxyproject D.O.T org mailing list, as it will reach the broadest Galaxy development community (not all review Biostars posts, instead they focus on the mailing list). If you are administering a Galaxy server, joining and following this list anyway could be very helpful.

More about mailing list choices:
http://wiki.galaxyproject.org/MailingLists

ADD REPLY • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

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