Basic bulk history file operations and tabular display missing from Galaxy?

Question: Basic bulk history file operations and tabular display missing from Galaxy?

3.2 years ago by

United Kingdom

uncoolbob • 10 wrote:

Hi all,

I'm a seasoned bioinformatics guy - have scripted NGS pipelines on HPC and so on - just trying to get my head around Galaxy...

One thing I'd like to do is bulk edit the file formats (via edit attributes) of the 20+ fastq files in my history to fastqsanger - can't seem to do that.

The other thing is, while I'm manually performing the above, where can I find a tabular display of history files with perhaps a user-configured set of columns (e.g. annotation, file format, size, creation date etc)? I would use this to check that I hadn't missed any files during the tedious manual process.

thanks!

Bob

galaxy • 712 views

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modified 3.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.2 years ago by uncoolbob • 10

3.2 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

As far as I know this is not possible. However, it should be possible in a data library, so you should do this before importing the data to your history and this is possible via the Galaxy API. So you can write a script to do this if you like.

ADD COMMENT • link written 3.2 years ago by Bjoern Gruening ♦ 5.1k

Thanks Bjoern, you're right that this should have been done at import time. I have a history shared to me by another user, however. All sorted now (manually in just a couple of minutes).

ADD REPLY • link written 3.2 years ago by uncoolbob • 10

3.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

A enhancement request ticket to add in more options to the existing "multiple dataset operations" function available in a history is here: https://trello.com/c/TxvMWp3r Please add in other operations that you think would be useful.

The second item is a very good idea. I created a new enhancement request ticket to create a new method/function that will generate a summary of dataset contents, including metadata and other key attributes related to format. Also please add in more information that you would like to see as part of this functionality. https://trello.com/c/9hw53h65

Thanks for the feedback! Jen, Galaxy team

ADD COMMENT • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

Nice - I'm signed up to the ticket system. Didn't know it was there.

As I said, I'm a newbie, but things are working out in Galaxy first time so far!

Thank you!

ADD REPLY • link written 3.2 years ago by uncoolbob • 10

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