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
14 months ago by
msprindzhuk50
msprindzhuk50 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 • 334 views
ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson25k • written 14 months ago by msprindzhuk50
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gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 13 months ago by Jennifer Hillman Jackson25k
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