[Sciapps-support] [External Email]Command line BSA-seq

[Wang, Liya]

Hi Frank,

Currently the workflow is not available via command line. To make it work locally, some parts of the workflow will have to be rewritten. The workflow is also supported by several databases built on our server which is not easy to distribute. I was thinking about re-architecting it but didn’t get the time yet. However, I could share individual components with you if you can let me know what you will need.

Regarding the API issues that blocks submitting new jobs on SciApps.org<http://SciApps.org>, I have contacted TACC support and hopefully will get problems figured out by tomorrow. Unfortunately TACC is currently closed due to the weather which also slows things down. Such issue has rarely happened before. Sorry for the inconvenience.

Regards,
Liya

On Feb 22, 2021, at 4:58 PM, Xin, Zhanguo - ARS <zhanguo.xin at usda.gov<mailto:zhanguo.xin at usda.gov>> wrote:

Dear Frank,

I think Liya can address your question.

Thanks,

Zhanguo Xin

Plant Stress & Germplasm Development Unit
USDA-ARS
3810 4th Street
Lubbock, TX 79415

Phone: (806)-749-5560
Fax: (806)-723-5272
E-mail: Zhanguo.Xin at ARS.USDA.GOV<mailto:Zhanguo.Xin at ARS.USDA.GOV>


From: Frank Harmon <fharmon at berkeley.edu<mailto:fharmon at berkeley.edu>>
Date: Monday, February 22, 2021 at 3:02 PM
To: Xin, Zhanguo - ARS <zhanguo.xin at usda.gov<mailto:zhanguo.xin at usda.gov>>
Subject: [External Email]Command line BSA-seq
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Dear Zhanguo,
A student and I are mapping one of the late flowering mutants with BSA-seq. SciApps is currently down. I am thinking about running the pipeline via command line. Is there code to run the bsa_viewer tool in this way?
I hope you faired okay during the cold spell there.
Sincerely,
Frank


——
Frank G. Harmon, PhD
Principal Investigator
Plant Gene Expression Center
Albany, CA








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