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

[Wang, Liya]

Hi Frank,

TACC has discover the issue that the Tapis API failed to retrieve the data from CyVerse Data Store to SciApps. They are trying to figure out how this can be resolved.

In the mean time, I was told by my CyVerse friend to make following changes to the sci_data folder via icommands before the API issue is resolved. I tested it and was able to launch jobs from SciApps.

ichmod -r own ipcservices /iplant/home/YOUR_CYVERSE_USER_NAME/sci_data

Just in case, here is the documentation for icommands: https://learning.cyverse.org/projects/data_store_guide/en/latest/step2.html

Regards,
Liya

On Feb 23, 2021, at 12:49 PM, Frank Harmon <fharmon at berkeley.edu<mailto:fharmon at berkeley.edu>> wrote:

Dear Liya,
I really appreciate your reply. I understand about the bsa-seq workflow. I expected this would be the case, but though it worth asking about. We can wait until SciApps is back up to map our mutant. Thank you for maintaining bsa-seq. It is such a great service!
Sincerely,
Frank

——
Frank Harmon
Plant Gene Expression Center
USDA-ARS & UC Berkeley

On Feb 23, 2021, at 7:50 AM, Wang, Liya <wangli at cshl.edu<mailto:wangli at cshl.edu>> wrote:

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<https://urldefense.proofpoint.com/v2/url?u=http-3A__sciapps.org_&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=VpyaB_1D0rsMuMrIznuCSA&m=CNeNWBUGcoupF0VNkh8NV_FwqS5OIYw3UyFlAKQ0uMs&s=DHvARSV4jkOA4sDBNm7f0T3wU2gtHP-0E6Su1LCSvkY&e=><http://SciApps.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__sciapps.org_&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=VpyaB_1D0rsMuMrIznuCSA&m=CNeNWBUGcoupF0VNkh8NV_FwqS5OIYw3UyFlAKQ0uMs&s=DHvARSV4jkOA4sDBNm7f0T3wU2gtHP-0E6Su1LCSvkY&e=>>, 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><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><mailto:Zhanguo.Xin at ARS.USDA.GOV>


From: Frank Harmon <fharmon at berkeley.edu<mailto: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><mailto:zhanguo.xin at usda.gov>>
Subject: [External Email]Command line BSA-seq
[External Email]
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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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