Question: Rename Tool Output File In Galaxy
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gravatar for Sachit Adhikari
5.1 years ago by
Sachit Adhikari320 wrote:
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
galaxy • 2.2k views
ADD COMMENTlink modified 5.1 years ago by Peter Cock1.4k • written 5.1 years ago by Sachit Adhikari320
0
gravatar for Peter Cock
5.1 years ago by
Peter Cock1.4k
European Union
Peter Cock1.4k 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 COMMENTlink written 5.1 years ago by Peter Cock1.4k
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 REPLYlink written 5.1 years ago by Sachit Adhikari320
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 REPLYlink written 5.1 years ago by Peter Cock1.4k
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 REPLYlink written 5.1 years ago by Sachit Adhikari320
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 REPLYlink written 5.1 years ago by Peter Cock1.4k
Thanks Peter for clearing this out.
ADD REPLYlink written 5.1 years ago by Sachit Adhikari320
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 REPLYlink written 5.1 years ago by fubar1.1k
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