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
- relates to
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IGBF-3035 Create Cyverse App to create and index Bedgraph
- Closed
Activity
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.
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)