Question: export workflow code
3.7 years ago by
guillaume.riviere • 0 wrote:
Hi there ,
How can I export my Galaxy workflow as code? I need the corresponding R script....
ADD COMMENT • link •modified 3.7 years ago by Martin Čech ♦♦ 4.9k • written 3.7 years ago by guillaume.riviere • 0
Can you please elaborate a little on your question? I am not sure I understand what you want to achieve.
A colleague of mine would like to get the workflow as an R script to combine her 'R' personal pipeline with galaxy worflow outputs in a single scripts so that all jobs are coordinated and she doesn't have to, for example, wait for a galaxy job to be finished before she can launch the R work. She'd rather lanch all and everything at once. Therefore she would like to know whether it is possible to export galaxy workflows as 'R-exploitables scripts' text files. The aim is to feed a single local R instance with BAM files without having to rewrite a R script containing the bioconductor tools that were organised in Galaxy (Not shure it gets clearer with those explanations..., sorry for that)...
Thanks a lot for your quick answers. You understood the issue perfectly. Thanks for your help!
Please accept the answer so others can benefit. Thanks.