I am new to Galaxy and NGS Data analysis in general. I was wondering if there is a way to to see the actual command line commands that Galaxy tools run on. For instance if I run Bowtie2 from the Galaxy interface is there a way to see how that particular job would look from the command line? Thanks for any input.
This is possible, but for security reasons only for Admin users. Press the [i]-icon in the history item and take a look at the first section. If you are admin you should see something like
Job Command-Line: ... right below
History API ID: ... and