Question: Command Line Access to Galaxy Tools
0
gravatar for caluga61
15 months ago by
caluga610
Stoneville
caluga610 wrote:

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.

api tool command line galaxy • 727 views
ADD COMMENTlink modified 15 months ago by y.hoogstrate450 • written 15 months ago by caluga610

I came across this older post: https://biostar.usegalaxy.org/p/6493/#6522. Does anyone know how to purposely cause a tool to fail?

ADD REPLYlink written 15 months ago by caluga610

Providing incorrect inputs is a simple way. Assign the expected datatype/database then adjust the dataset content to be invalid.

Or for many tools, the command-line is now reported on the "i" info page for any dataset (successful or not). If that is available for target tools, it is a quick way to see the command-line structure.

ADD REPLYlink modified 15 months ago • written 15 months ago by Jennifer Hillman Jackson23k
1
gravatar for y.hoogstrate
15 months ago by
y.hoogstrate450
Netherlands
y.hoogstrate450 wrote:

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 UUID: ....

ADD COMMENTlink written 15 months ago by y.hoogstrate450
0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Another option is to use the API. https://wiki.galaxyproject.org/Develop/API

Best, Jen, Galaxy team

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson23k
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