is there a simple way to access an arbitrary dataset's absolute path?
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*
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.html<http://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/
______________________________**_____________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- 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*
participants (2)
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Hans-Rudolf Hotz -
W. Augustine Dunn III