Details
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Type:
Bug
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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: 9.0.2 Minor Release
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Labels:
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Story Points:1
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Sprint:Fall 2018 Sprint 2, Fall 2018 Sprint 3
Description
Identify GNC & Ecker data sets on HPC cluster and deploy to new ChIP-Seq data repository.
Note: data may still be available on old transvar Andrew File System previously hosted in DHMRI server room. Data may also be available on transvar VM Blanchard set up following loss of DHMRI server room. Consult with Steven Blanchard to obtain backups, if they exist.
When complete, be sure to update basecamp project(s) about where to find data.
Attachments
Issue Links
- relates to
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IGBF-1403 Add DNA-Seq and ChIP-Seq Quickload sources
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- Closed
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Activity
I'm moving this to "needs first level review" and keeping it assigned to myself.
That seems fitting because I'm doing working on it, but I still need to hear back from Eric and Ann about the final details before I can call it "done", and they could conceivably kick it back for changes.
GNC, EIN3 data added to: http://lorainelab-quickload.scidas.org/chipseq/
Moved unpublished data to new hosting (ask Dr. Loraine for URL)
To test:
- Add above link as new data source using IGB Data Access tab
- Visit Arabidopsis genome
- Open ChIP-Seq data set
- Check that all files in the following data set folders can be loaded.
Data sets to check:
- GNC PRJNA435725
- EIN3 PRJNA185404
- ARR10 PRJNA263839
If any files cannot be loaded, report them here. In your report, include:
- The path to the physical file on the host (file attribute in annots.xml)
- The data set name as listed in the IGB user interface (title attribute in annots.xml)
The "annots.xml" file is here: http://lorainelab-quickload.scidas.org/chipseq/A_thaliana_Jun_2009/annots.xml
While testing, error message as given below was shown on IGB:
Could not load feature:
The feature http://lorainelab-quickload.scidas.org/chipseq/A_thaliana_Jun_2009/ARR10_SRP048935/SRR1613114.bam is not reachable.
1. file name= "ARR10_SRP048935/SRR1612835.bam"
title="ARR10 PRJNA263839/alignments/line a1 BA-treated ChIP rep1 alignments"
2. file name="ARR10_SRP048935/SRR1613114.bam"
title="ARR10 PRJNA263839/alignments/line a1 BA-treated non-IP rep1 alignments"
3. file name="ARR10_SRP048935/SRR1613116.bam"
title="ARR10 PRJNA263839/alignments/line a1 BA-treated ChIP rep2 alignments"
4. file name="ARR10_SRP048935/SRR1613117.bam"
title="ARR10 PRJNA263839/alignments/line a1 BA-treated non-IP rep2 alignments"
Thanks for catching this Pranav!
For future reference, problem was due to incorrect file permissions setting - files above were not world-readable.
This is now fixed.
I sent Steven an email.