Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Extract command line from Galaxy run?
0
gravatar for daniel.tonge
21 months ago by
daniel.tonge • 10
daniel.tonge • 10 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 • 581 views
ADD COMMENT • link •
written 21 months ago by daniel.tonge • 10
0
gravatar for Devon Ryan
21 months ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k 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 COMMENT • link written 21 months ago by Devon Ryan • 1.9k

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 REPLY • link written 21 months ago by Wolfgang Maier • 600

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

ADD REPLY • link modified 21 months ago • written 21 months ago by Guy Reeves • 1.0k

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

ADD REPLY • link written 21 months ago by Devon Ryan • 1.9k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 180 users visited in the last hour