Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: export workflow code
0
gravatar for guillaume.riviere
3.7 years ago by
guillaume.riviere • 0
France
guillaume.riviere • 0 wrote:

Hi there ,

How can I export my Galaxy workflow as code? I need the corresponding R script....

Thanks

Guillaume
workflow export • 1.0k views
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.

ADD REPLY • link written 3.7 years ago by Martin Čech ♦♦ 4.9k

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)...

Thx

Guillaume.

ADD REPLY • link written 3.7 years ago by guillaume.riviere • 0

Martin,

Thanks a lot for your quick answers. You understood the issue perfectly. Thanks for your help!

Guillaume

 

ADD REPLY • link written 3.7 years ago by guillaume.riviere • 0

Please accept the answer so others can benefit. Thanks.

ADD REPLY • link written 3.7 years ago by Martin Čech ♦♦ 4.9k
2
gravatar for Martin Čech
3.7 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

From what I understand about your question, and my understanding may be flawed, you are trying to flatten galaxy workflow into a script. It might be difficult but possible for some workflows but there is no way to automate that process through Galaxy. For many workflows this would be close to impossible task.

My advice is to create a Galaxy Tool from your colleague's R script instead and add it to the Galaxy Workflow. That is what Galaxy is designed to do.
ADD COMMENT • link written 3.7 years ago by Martin Čech ♦♦ 4.9k
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: 174 users visited in the last hour