Hi Lilach,
Often tools will report the command line in the comments after a job has completed, but not always. Including the full command string with all tools is a goal
But until then, there is a way to get it for all tools (or nearly all) via a very special method. Please stay with me here - it is by purposely /causing the tool to fail/ (really error -> turn dataset red), then clicking on the green bug icon as if to submit a bug report. Sometimes the command string is available in the stdout/stderr in the bug report or "i" info page and you do not need to actually submit it - you can just review the report and data. Other times, you will need to submit it and wait for the email copy of that report to be cc'd to you. In the bug report the full command string as executed will be reported about 1/3 of the way down in the email.
I use this exact same information every day to help people solve problems - it is very informative, especially for folks with a bioinformatics background who just need to know the exact details or those wanting to make the full connection between tool form and command-line options. This information is saved/available in every single job, so no one should be concerned that only error jobs have this sort of information recorded. _All jobs are perfectly reproducible at this level_, the extreme detail is just not in the UI display for all - yet.
When you are doing this to just capture command strings (submitting bug reports), please include a note in the comments stating to ignore the bug report, e.g. "that it was on purpose - ignore!", and we'll ignore, no problem! :)
The "error" is also reported in the logs, but as noted earlier in this thread, you won't have access to that on external servers. Combined with the wrapper and source code at galaxy-central, 3rd party sites, and the tool shed, this should give you both the full access and the autonomy you want to learn from existing tools as implemented on Test and Main (and perhaps other sources - you'll have to check each for the bug report settings/policies).
Hope this helps!
Jen Galaxy team
On 8/27/13 5:29 AM, lilach noy wrote:
Hello,
How can i see the command line a query executes? To be more specific i am new to the Galaxy and plan to use as a way to learn how to run queries locally. In order to understand not only the functions available but also the way i can write it on my own i'd be happy to be able to see the command line that execute my queries. How can I see this?
Thank you
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