Avoid to download output files
Hi, I don't want dowload the output files which Galaxy generates, because I don't want to have them in double in my disk. I saw, that the output files are in file_path an I found them. But they have a .dat extension ! In your mailing-list archive I haven't found a solution to transform these extensions. Is it possible to change this with a simple change in a configuration file or in a script file ? Or, must I write my owner script, and if yes, how can I configure Galaxy so that it launches it automatically after one application like MACS for exemple which have a file configuration : macs.xml in the tools directory? Because I've tried to add a line like this in this file : <command interpreter ="perl"> mon scrip.pl</command> I've placed it after the line <command...> which launches the MACS script, but my script seems not work. Thank you. julie
Is it possible to change this with a simple change in a configuration file or in a script file ?
No, they must be named as is for Galaxy to find them. You could, however, create symbolic links to files and use an extension of your choice.
Or, must I write my owner script, and if yes, how can I configure Galaxy so that it launches it automatically after one application like MACS for exemple which have a file configuration : macs.xml in the tools directory? Because I've tried to add a line like this in this file : <command interpreter ="perl"> mon scrip.pl</command> I've placed it after the line <command...> which launches the MACS script, but my script seems not work.
It's not possible to launch Galaxy automatically on local files. You'll need to upload the file to Galaxy and run the tool using the uploaded file as input. Hopefully I answered your question; if not, can be more specific about what you're trying to do? Best, J.
Thank you Jeremy, you answered partially. I would like insert a command, to launch my script, in the script or in the xml files of my tools to force it to change the extension of output files. But it seems impossible because my command perl after the command of tool's script doesn't work in xml file. I think, I will use your first proposition with symbolic links. Thank you. Julie 2012/5/24 Jeremy Goecks <jeremy.goecks@emory.edu>
Is it possible to change this with a simple change in a configuration file or in a script file ?
No, they must be named as is for Galaxy to find them. You could, however, create symbolic links to files and use an extension of your choice.
Or, must I write my owner script, and if yes, how can I configure Galaxy so that it launches it automatically after one application like MACS for exemple which have a file configuration : macs.xml in the tools directory? Because I've tried to add a line like this in this file : <command interpreter ="perl"> mon scrip.pl</command> I've placed it after the line <command...> which launches the MACS script, but my script seems not work.
It's not possible to launch Galaxy automatically on local files. You'll need to upload the file to Galaxy and run the tool using the uploaded file as input.
Hopefully I answered your question; if not, can be more specific about what you're trying to do?
Best, J.
Thank you Jeremy, you answered partially. I would like insert a command, to launch my script, in the script or in the xml files of my tools to force it to change the extension of output files. But it seems impossible because my command perl after the command of tool's script doesn't work in xml file.
The key thing to know is that Galaxy creates a single command line when running a tool, not a script. So, to add your command to a tool, you could try adding a semi-colon as a separator and then your command. E.g. ...; python my_prog.py [inputs] Best, J.
On Thu, May 24, 2012 at 1:54 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Julie wrote:
Thank you Jeremy, you answered partially. I would like insert a command, to launch my script, in the script or in the xml files of my tools to force it to change the extension of output files. But it seems impossible because my command perl after the command of tool's script doesn't work in xml file.
The key thing to know is that Galaxy creates a single command line when running a tool, not a script. So, to add your command to a tool, you could try adding a semi-colon as a separator and then your command. E.g.
...; python my_prog.py [inputs]
Could multiple <command> entries be flagged as an error in the loader? That would have helped with Julie's first attempt. Alternatively, could we have a DTD file for the wrappers to use, and then an XML editor would be able to spot this kind of mistake? Regards, Peter
Ok I've tried to add my script perl in the command line with semi-colon. It's work But this script sets in entry the variable $wigoutput of my file xml. But when I show it, it's not what I want; It's just the value : 1 . I think it's because the script of the application (macs) is called before my script, the $wigoutput doesn't contain the good value when it stops. It is what I think, it's not possible to change the extension. Thank you for your attention and your answers Julie 2012/5/24 Jeremy Goecks <jeremy.goecks@emory.edu>
Thank you Jeremy, you answered partially. I would like insert a command, to launch my script, in the script or in the xml files of my tools to force it to change the extension of output files. But it seems impossible because my command perl after the command of tool's script doesn't work in xml file.
The key thing to know is that Galaxy creates a single command line when running a tool, not a script. So, to add your command to a tool, you could try adding a semi-colon as a separator and then your command. E.g.
...; python my_prog.py [inputs]
Best, J.
On Thu, May 24, 2012 at 3:27 PM, julie dubois <dubjulie@gmail.com> wrote:
Ok I've tried to add my script perl in the command line with semi-colon. It's work But this script sets in entry the variable $wigoutput of my file xml. But when I show it, it's not what I want; It's just the value : 1 . I think it's because the script of the application (macs) is called before my script, the $wigoutput doesn't contain the good value when it stops. It is what I think, it's not possible to change the extension.
Thank you for your attention and your answers Julie
Well, yes, if you do this at the command line: cmdA; cmdB then cmdA is executed before cmdB. Try it yourself at the Unix/Linux prompt, e.g. date; ls compared to: ls; date If you want to run it first, try putting your script BEFORE the existing entry in the tool XML's <command> tag. Peter
It works !!! I've changed the extension of output file of an application. But in Galaxy, it's referenced over the old file with .dat in history, so if we want to re-use this file with other tool it's not the best way to change this extension after the run of tool. If I could change the extension before the chargement in history, that would be perfect. But I suppose it's not possible. I'm already satisfied of the possibility I've discover with the modification of xml files. Thank you for your help Julie 2012/5/24 Peter Cock <p.j.a.cock@googlemail.com>
On Thu, May 24, 2012 at 3:27 PM, julie dubois <dubjulie@gmail.com> wrote:
Ok I've tried to add my script perl in the command line with semi-colon. It's work But this script sets in entry the variable $wigoutput of my file xml. But when I show it, it's not what I want; It's just the value : 1 . I think it's because the script of the application (macs) is called before my script, the $wigoutput doesn't contain the good value when it stops. It is what I think, it's not possible to change the extension.
Thank you for your attention and your answers Julie
Well, yes, if you do this at the command line:
cmdA; cmdB
then cmdA is executed before cmdB.
Try it yourself at the Unix/Linux prompt, e.g.
date; ls
compared to:
ls; date
If you want to run it first, try putting your script BEFORE the existing entry in the tool XML's <command> tag.
Peter
participants (3)
-
Jeremy Goecks -
julie dubois -
Peter Cock