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Command Line in Galaxy

I am new to Galaxy and NGS data analysis in general. I was wondering, is there a way to view the command line commands that are running the Galaxy tools? For instance if I run Bowtie2 in Galaxy, is there a way to see how that instance of Bowtie2 would look if ran from command line? Thanks for any input.

command line
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updated by Biostar Biostar • written by caluga61 • caluga61

Does not appear that you can (any longer?). At least on PSU galaxy. I see that you have posted this question over on Galaxy Biostars as well (was going to suggest that).

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written by GenoMax GenoMax

Bad input can sometimes do the trick since many programs don't check/validate their input (but Galaxy may do it for them instead though)

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written by Jean-Karim Heriche Jean-Karim Heriche

Normally you have to be logged in as an admin for that to appear. I agree this is annoying. In fact, it even bothers me as an admin since I sometimes have to "impersonate" users (i.e., run Galaxy as them) in order to debug things...but then I can no longer see the commands getting sent to the queue without using ssh (or a different browser). If I remember I'll ask someone tomorrow about this, since I'm at a Galaxy conference at the moment.

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written by Devon Ryan Devon Ryan

Hello caluga61!

We believe that this post does not fit the main topic of this site.

Better place to ask this: https://biostar.usegalaxy.org

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by Michael Dondrup Michael Dondrup

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