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Question: Command Line Access to Galaxy Tools
0
gravatar for caluga61
2.1 years ago by
caluga61 • 0
Stoneville
caluga61 • 0 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 • 1.4k views
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modified 2.1 years ago by y.hoogstrate • 460 • written 2.1 years ago by caluga61 • 0

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 REPLY • link written 2.1 years ago by caluga61 • 0

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 REPLY • link modified 2.1 years ago • written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k
1
gravatar for y.hoogstrate
2.1 years ago by
y.hoogstrate • 460
Netherlands
y.hoogstrate • 460 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 COMMENT • link written 2.1 years ago by y.hoogstrate • 460
0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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

Best, Jen, Galaxy team
ADD COMMENT • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k
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