Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:0.5
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Epic Link:
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Sprint:Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25, Spring 5 2022 Feb 28 - Mar 11, Spring 6 2022 Mar 14 - Mar 25, Spring 7 2022 Mar 28 - Apr 8
Description
Karthik Raveendran has created a new Docker image containing deepTools, tabix (samtools), and a custom script he wrote to enable running of the image in CyVerse environment to compute a scaled coverage graph file (bedgraph format) and then tabix-index it.
He's run into some problems with getting the new image to run as wanted in the environment.
He will send a email asking about this to the CyVerse team and record the answers and insights obtained here.
Questions:
- How do I get access to the condor stderr and stdout ?
- How do I add metadata tags to my app even while it's in my private account and not yet widely available, i.e., "published"
This may be helpful:
IGB class information about using the IGB Docker image to build IGB:
https://canvas.instructure.com/courses/1164217/pages/learn-to-use-igb-docker-image-build-environment?module_item_id=43241015
Attachments
Issue Links
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- Closed
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Activity
[~aloraine] - It may be worth contacting Sriram Srinivasan and seeing if he would be willing to meet up or have a zoom call. He is located in Cary, NC, so he is not far from us.
Software Engineer Lead, Core Software, University of Arizona | sriram@cyverse.org | https://cyverse.org/team
Linkedin profile: https://www.linkedin.com/in/sriramsrinivasan83/
I sent and email to Sriram in Cyverse with an image attachment (added here as well):
"I am part of the BioViz Connect Team from the Genome Visualization Lab in Charlotte. I was trying to deploy an app in Cyverse using the tool bam2tbi and the job keeps failing. I checked the logs for ‘condor_stderr’ file and ‘condor_stdout’ file but it was not there. I made changes to the docker file, assuming what could be the errors and it continued to fail. I was really hoping to get some help with this. Thank you in advance.
Moreover, I was wondering how to add the ‘Argument’ parameter in the Cyverse app if its possible. I have attached an image of an app that the Cyverse team had created for us which illustrates what I mean by the ‘Argument’ parameter
Regards,
Karthik Raveendran"
Any answer Karthik Raveendran?
I have not received a reply for the above.
As per scrum discussion today, closing this ticket as we are not getting a reply from CyVerse support. We will revisit when we have greater need to create new CyVerse apps.
Also, let's be sure to attend any new tutorials at conferences on how to create apps. (comment from Karthik Raveendran)
Cyverse support team was contacted yesterday via the chat module regarding the questions in the description. They did not reply so a mail was sent to support@cyverse.org. Meanwhile, in the Cyverse app, bam2tbi, I was able to send file path to the input parameter but the image stopped running. I was not able to discern the nature to the error.