Rename Tool Output File In Galaxy

Question: Rename Tool Output File In Galaxy

5.4 years ago by

Hi group, The galaxy stores the output of the job on files/043/dataset_*ID*.dat. I have two questions here.: 1) Can I find the ID of my output from the Galaxy history? I tried Edit Attributes, Annotations, tags but couldn't find it. 2) Can I rename my output while initiating the task? If I can how can I do this and what are the consequences. Thank you. Regards, Sachit

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modified 5.4 years ago by Peter Cock • 1.4k • written 5.4 years ago by Sachit Adhikari • 320

5.4 years ago by

Peter Cock • 1.4k

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Peter Cock • 1.4k wrote:

On Wed, Jul 24, 2013 at 5:21 AM, Sachit Adhikari Via the "i" icon of a history entry (information) you can see the datafile's full path which includes the ID. Yes, you can. Normally this is fine. (Note sure if there can be complications with meta-data normally added automatically by inspecting the finished file...) Peter

ADD COMMENT • link written 5.4 years ago by Peter Cock • 1.4k

Hi, By "i" do you mean Edit attributes button? There are four sub-headings on that: Attributes, Convert format, Datatype and permissions but I can't see data file's full path on any of them. What's wrong?

ADD REPLY • link written 5.4 years ago by Sachit Adhikari • 320

On Wed, Jul 24, 2013 at 10:35 AM, Sachit Adhikari No, not the edit button. First click on a dataset's title so it expands. You should see a snippet of data etc plus a row of icons (save, information, reload in bottom left of the history, and tags and annotation bottom right). Peter

ADD REPLY • link written 5.4 years ago by Peter Cock • 1.4k

Yes, but unfortunately that didn't work too. I have already tried the solution you provided. I could edit the tags and annotations but it won't change the file name in my file system. The file is still named as * "dataset_43649.dat". *

ADD REPLY • link written 5.4 years ago by Sachit Adhikari • 320

On Wed, Jul 24, 2013 at 11:15 AM, Sachit Adhikari You *cannot* rename the file on disk (without bypassing Galaxy and editing the database and renaming the file directly). This is by design - unless you are an administrator debugging something or a tool author you don't need to know the actual filename on disk. You *can* rename the description of the file as shown within the Galaxy interface (via edit attributes). Peter

ADD REPLY • link written 5.4 years ago by Peter Cock • 1.4k

Thanks Peter for clearing this out.

ADD REPLY • link written 5.4 years ago by Sachit Adhikari • 320

Sachit, that's a feature, not a bug. Changing the name of a file on disk being managed by Galaxy is unlikely to have a happy ending. The pencil icon allows changes to the history display name but the disk file name needs to be left alone. On Wed, Jul 24, 2013 at 8:15 PM, Sachit Adhikari < -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ

ADD REPLY • link written 5.4 years ago by fubar ♦ 1.1k

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