Watching Command Line To A Query

Question: Watching Command Line To A Query

5.3 years ago by

lilach noy • 100

lilach noy • 100 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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modified 5.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.3 years ago by lilach noy • 100

5.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 5.3 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, This would be very useful for users who don't have access to Galaxy logs. Could you please describe in additional detail how (sequence of steps) to cause a tool to fail in order to make the bug icon appear ? I am assuming you can, through the method you suggested, cause a tool/job that would normally have succeeded to fail instead. Thanks. Date: Thursday, August 29, 2013 8:30 PM To: lilach noy <lilachnoy@gmail.com<mailto:lilachnoy@gmail.com>> Cc: "galaxy-user@bx.psu.edu<mailto:galaxy-user@bx.psu.edu>" <galaxy- user@bx.psu.edu<mailto:galaxy-user@bx.psu.edu="">> Subject: Re: [galaxy-user] watching command line to a query 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 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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD REPLY • link written 5.2 years ago by Srinivas • 50

5.3 years ago by

Srinivas • 50

United States

Srinivas • 50 wrote:

Hi Lilach, One method would be by checking the contents of the log file for entries such as "submitting file /Groups/Galaxy/galaxy- dist/database/pbs/galaxy_48152.sh". The contents of the file listed contain the command line issues by Galaxy. Date: Tuesday, August 27, 2013 7:29 AM To: "galaxy-user@bx.psu.edu<mailto:galaxy-user@bx.psu.edu>" <galaxy- user@bx.psu.edu<mailto:galaxy-user@bx.psu.edu="">> Subject: [galaxy-user] watching command line to a query 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

ADD COMMENT • link written 5.3 years ago by Srinivas • 50

Thank you for the reply. Where can i find the log file? 2013/8/27 Maddhi, Srinivas <srinivas-maddhi@uiowa.edu>

ADD REPLY • link written 5.3 years ago by lilach noy • 100

As an ordinary Galaxy user, I'm not sure if this is possible. You would have to be running your own Galaxy instance, look at the file paster.log in the main Galaxy folder. Peter

ADD REPLY • link written 5.3 years ago by Peter Cock • 1.4k

And if I use the web interface? can I watch the command line there? 2013/8/27 Peter Cock <p.j.a.cock@googlemail.com>

ADD REPLY • link written 5.3 years ago by lilach noy • 100

I don't believe so. Peter is right -- I forgot to mention that you would need read access to the log files on the server running Galaxy. It would be nice if Galaxy were able to display the command issued, unless it already does and I am not aware of it, without requiring such access (perhaps as an additional row in the "View details" screen). Date: Tuesday, August 27, 2013 8:17 AM To: Peter Cock <p.j.a.cock@googlemail.com<mailto:p.j.a.cock@googlemail.com>> Cc: Srinivas Maddhi <srinivas-maddhi@uiowa.edu<mailto:srinivas- maddhi@uiowa.edu="">>, "galaxy-user@bx.psu.edu<mailto:galaxy- user@bx.psu.edu="">" <galaxy-user@bx.psu.edu<mailto:galaxy- user@bx.psu.edu="">> Subject: Re: [galaxy-user] watching command line to a query And if I use the web interface? can I watch the command line there? 2013/8/27 Peter Cock <p.j.a.cock@googlemail.com<mailto:p.j.a.cock@googlemail.com>> As an ordinary Galaxy user, I'm not sure if this is possible. You would have to be running your own Galaxy instance, look at the file paster.log in the main Galaxy folder. Peter

ADD REPLY • link written 5.3 years ago by Srinivas • 50

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