Question: Basic bulk history file operations and tabular display missing from Galaxy?
gravatar for uncoolbob
3.2 years ago by
United Kingdom
uncoolbob10 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.



galaxy • 712 views
ADD COMMENTlink modified 3.2 years ago by Jennifer Hillman Jackson25k • written 3.2 years ago by uncoolbob10
gravatar for Bjoern Gruening
3.2 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k 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 COMMENTlink written 3.2 years ago by Bjoern Gruening5.1k

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 REPLYlink written 3.2 years ago by uncoolbob10
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


A enhancement request ticket to add in more options to the existing "multiple dataset operations" function available in a history is here: 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.

Thanks for the feedback! Jen, Galaxy team


ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k

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 REPLYlink written 3.2 years ago by uncoolbob10
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