Details
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Type: Task
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Status: Testing Complete (View Workflow)
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Priority: Major
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Resolution: Done
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Fall 5 : 14 Oct to 25 Oct
Description
Situation: Samtools HTSJDK requires that a bai file have a bam file with the same name and in the same directory. However, IGB Quickload annots.xml has/had the ability to specify a bam file and index in two separate locations.
Task: Create an example quickload to test the ability of annots.xml to specify a bam and index that exist in two separate folders. Also test if the names of the bam file and index can be different.
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Nowlan Freese
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Nowlan Freese
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Nowlan Freese
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Status | Open [ 1 ] | To-Do [ 10305 ] |
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Status | To-Do [ 10305 ] | In Progress [ 3 ] |
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Attachment | 854.png [ 14442 ] | |
Attachment | 900.png [ 14443 ] | |
Attachment | 902.png [ 14444 ] | |
Attachment | 910.png [ 14445 ] | |
Attachment | quickloads.zip [ 14446 ] |
Nowlan Freese
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Nowlan Freese
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Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Nowlan Freese
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Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
Ann Loraine
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Workflow | Fall 2019 Workflow Update [ 20824 ] | Revised Fall 2019 Workflow Update [ 21161 ] |
Ann Loraine
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Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
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Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Ann Loraine
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Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Ann Loraine
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Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Ann Loraine
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Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
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Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
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Resolution | Done [ 10000 ] | |
Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Ann Loraine
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Assignee | Ann Loraine [ aloraine ] | Nowlan Freese [ nfreese ] |
Ann Loraine
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Created multiple quickloads to test if the index attribute in annots.xml is functioning correctly in quickloads.
Tested IGB 8.5.4, 9.0.0, 9.0.2, and 9.1.0 (see attached images) as of October 15, 2019.
The index attribute only works if the full URI is specified to the data. For example, having a local or remote quickload that specifies the full path to remotely hosted data works correctly (all files load).
If the index attribute is specified and the data use relative URIs, data do not load correctly. For example, a local quickload with local data using relative URIs can only load a bam file with a bai in the same folder with the same name. Interestingly, if the quickload is in Amazon with the data also stored in amazon with relative URIs, none of the data is able to load, including the bam/bai in the same folder and with the same name.
If the index attribute is omitted, a quickload in amazon using relative URIs can load the bam/bai in the same folder and with the same name, which is how our current IGB quickloads are designed.
To test:
Unzip the attached quickloads.zip and add the two local quickloads and the following remote quickloads in the configure data panel:
https://quickload-testing.s3.amazonaws.com/QL_Amazon_Target_CyVerse
https://quickload-testing.s3.amazonaws.com/QL_Amazon_Target_Amazon
https://quickload-testing.s3.amazonaws.com/QL_Amazon_Target_Amazon_noIndex
Next, go to the Arabidopsis genome, chromosome 1, zoom all the way in, and go to the beginning position of the chromosome. Select the files from the quickloads and load data.