Question: Extract command line from Galaxy run?
0
gravatar for daniel.tonge
14 months ago by
daniel.tonge10
daniel.tonge10 wrote:

Just a quick thought...

I tend to run RNA-seq locally, whilst my PhD students may use Galaxy for convenience. Is there anyway that I can extract the command that underlies their Galaxy run, so that I could easily replicate what they have done locally (i.e. on a standard Linux server setup)??

Much appreciated.

D

rna-seq tophat galaxy • 387 views
ADD COMMENTlink written 14 months ago by daniel.tonge10
0
gravatar for Devon Ryan
14 months ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:

Are you an admin on the Galaxy instance they're using? The command line is stored in the database. If you're not, startup a docker container with docker-galaxy-stable, install whatever they need, and have them run one sample. You can then just look at what the command is in top.

ADD COMMENTlink written 14 months ago by Devon Ryan1.9k

Are you an admin on the Galaxy instance they're using? The command line is stored in the database.

... and is exposed to admin users under "View Details" of any Dataset.

ADD REPLYlink written 14 months ago by Wolfgang Maier530

Isn't this info available to non-admin user through the same veiw details button?

ADD REPLYlink modified 14 months ago • written 14 months ago by Guy Reeves1.0k

The options in the wrapper are displayed, but not the command that's actually run (only admins see that).

ADD REPLYlink written 14 months ago by Devon Ryan1.9k
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