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Question: How to run preformed Galaxy pipeline programmatically and dynamically change pipeline`s parameters like new SRA identifier?
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gravatar for msprindzhuk
19 months ago by
msprindzhuk • 50
msprindzhuk • 50 wrote:

How to run preformed Galaxy pipeline programmatically and dynamically change pipeline`s parameters like SRA identifier?

Need to run a pipeline on an input of 500 new SRA identifiers. Is it possible using Bioblend, Python and Galaxy`s API?
sra bioblend api pipeline batch • 495 views
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modified 18 months ago by Jennifer Hillman Jackson ♦ 25k • written 19 months ago by msprindzhuk • 50
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gravatar for Jennifer Hillman Jackson
18 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you are using the tools in the group NCBI SRA Tools, single or multiple accession can be processed as an input to extract data in batch. This input type a text file of accession IDs, in list format, one accession per line.

Should you have a different use case, please provide more details and potentially a shared link to the workflow and a history that contains the inputs and optionally a test run of the workflow (if the workflow/history is at http://usegalaxy.org or you upload that content there).

Share links can be posted here as a reply comment or sent in directly to galaxy-bugs@lists.galaxyproject.org. Using the email list would keep your data private, but would not allow others from the wider Galaxy community to provide feedback/troubleshooting help. If you do email the share link(s), please include details plus a link to this post so we can associate the two. It is best if to send this from your registered Galaxy account email address.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k
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