Hello all:
There are times when I want to explore data produced inside my local galaxy site without using galaxy tools. For example, I may want to run a custom script or even just a grep type function from the command line on a couple CuffDiff output files to get an idea of whats inside.
This requires a way to get the absolute path to that dataset as it lives in galaxy's internal structure. The only way that I have found to do this is to place this dataset in the shared_data/data_libraries and then view this dataset's info as admin. This is not practical for the types of things I want to do (simple one-off old-school command line investigations on arbitrary files).
Is there a way for me to add this info to the standard "view info" page format of datasets so that I can do this sort of thing easily? Mind you, I am not planning to alter the data in galaxy, just look at it and sometimes dump a summary table to a folder outside of galaxy's domain.
Thanks,
Gus
Hi Gus
Have a look at Shantanu's email from last October:
http://dev.list.galaxyproject.org/displaying-dataset-paths-in-the-UI-td41420...
It works very well for us.
Regards, Hans
On 04/05/2012 08:46 PM, W. Augustine Dunn III wrote:
Hello all:
There are times when I want to explore data produced inside my local galaxy site without using galaxy tools. For example, I may want to run a custom script or even just a grep type function from the command line on a couple CuffDiff output files to get an idea of whats inside.
This requires a way to get the absolute path to that dataset as it lives in galaxy's internal structure. The only way that I have found to do this is to place this dataset in the shared_data/data_libraries and then view this dataset's info as admin. This is not practical for the types of things I want to do (simple one-off old-school command line investigations on arbitrary files).
Is there a way for me to add this info to the standard "view info" page format of datasets so that I can do this sort of thing easily? Mind you, I am not planning to alter the data in galaxy, just look at it and sometimes dump a summary table to a folder outside of galaxy's domain.
Thanks,
Gus
-- In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. /-Stephen Jay Gould/
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Brilliant!
On Tue, Apr 10, 2012 at 1:19 AM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Gus
Have a look at Shantanu's email from last October:
http://dev.list.galaxyproject.**org/displaying-dataset-paths-** in-the-UI-td4142007.htmlhttp://dev.list.galaxyproject.org/displaying-dataset-paths-in-the-UI-td4142007.html
It works very well for us.
Regards, Hans
On 04/05/2012 08:46 PM, W. Augustine Dunn III wrote:
Hello all:
There are times when I want to explore data produced inside my local galaxy site without using galaxy tools. For example, I may want to run a custom script or even just a grep type function from the command line on a couple CuffDiff output files to get an idea of whats inside.
This requires a way to get the absolute path to that dataset as it lives in galaxy's internal structure. The only way that I have found to do this is to place this dataset in the shared_data/data_libraries and then view this dataset's info as admin. This is not practical for the types of things I want to do (simple one-off old-school command line investigations on arbitrary files).
Is there a way for me to add this info to the standard "view info" page format of datasets so that I can do this sort of thing easily? Mind you, I am not planning to alter the data in galaxy, just look at it and sometimes dump a summary table to a folder outside of galaxy's domain.
Thanks,
Gus
-- In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. /-Stephen Jay Gould/
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Hans-Rudolf Hotz -
W. Augustine Dunn III