Question: Invoking galaxy workflows via API and providing fastq as input file
gravatar for singhbanipal
11 months ago by
singhbanipal0 wrote:

Hi All,

I'm very new to Galaxy world and looking for your kind help on below points:

  1. Any article or example as how to use API to trigger workflow ?
  2. How to upload and use particular file while invoking WorkFlow via API?
  3. How to execute workflow in synchronous manner?


workflow api • 426 views
ADD COMMENTlink modified 11 months ago by bensellak0 • written 11 months ago by singhbanipal0

Thanks for your response @Martin...

Is it only way to go via bioblend there any other way available to interact with Galaxy via REST calls?

I do see some of below apis are available but I'm not sure how to define inputs to them and trigger our workflows...Can you please help me with this? https://host:80/api/workflows/ GET : To get related workflows POST: To trigger particular workflow

any example related to this will be helpful.


ADD REPLYlink written 11 months ago by singhbanipal0

You surely can use the whole raw Galaxy's API - the documentation is here:

For more details and examples please see the hub page

ADD REPLYlink written 11 months ago by Martin Čech ♦♦ 4.9k
gravatar for Martin Čech
11 months ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

The bioblend library is usually a very good companion when working with Galaxy's API.

  1. see the docs on how to invoke a workflow
  2. Uploading a file via API can be done via this method
  3. Could you please elaborate what you mean by synchronous execution in this context?
ADD COMMENTlink written 11 months ago by Martin Čech ♦♦ 4.9k
gravatar for bensellak
11 months ago by
bensellak0 wrote:

Going through the galaxy's API is the hard way. You can use existing python libraries such Bioblend. You can connect to your galaxy instance by API key, first upload your files just by calling the upload tool, then the rest is quite the same. Prepare you inputs for each tool an run it. It will be better if you execute the whole thing as a workflow.

ADD COMMENTlink written 11 months ago by bensellak0

Thanks for guidance @Bensellak,

Somehow I'm able to follow you for bioblend. Even I was also trying on same side but facing issue with below two things: 1. how to create URL for each of the Bioblend python script to expose for HTTP hit? 2. I was trying to trigger some workflows with /api/workflows, I'm not getting to create required INPUT Json. Considering I dont have functional knowledge on WorkFlows, is there any way I can get information as how to define these input Json structures for whole flow?

I'm stuck here, please help me with some break thru.


ADD REPLYlink written 10 months ago by singhbanipal0
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