I sent Steven an email.

Stephen replied. There is a backup.

I copied the backup to my local machine using sftp.

I created an EBS volume and attached it to my test quickload EC2 instance (http://18.222.191.240/).

I copied everything but the ARR10_cytokinin project into this EBS volume.
(this means I will need to update to the annots file to not include that project.)

I moved the EBS volume within the EC2 instance to a web-accessible directory.
The restored schallerlab quickload can now be added to IGB data sources using: http://18.222.191.240/Quickload_schallerlab/

I need to add password protection.
And I need to replace the current annots file with the reduced version (no ARR10_cytokinin).
Then this will be in a state that Eric could use in the short term.

I will need to separate out the GNC files with an annots file for just that project for Ann to add to the chip-seq repository.

At this point, I have exchanged several emails with Ann and Eric.
The ARR10 ethylene dataset is still in some flux. It will probably move to RECI without password protection, but Eric still needs to approve that plan (awaiting reply email).
The GNC and Ecker ChIP-Seq data are on the EBS volume, for testing and they look good. They are available on the HPC cluster under
/nobackup/lorainelab/data/GNCChIP-Seq/Quickload_Site/Quickload_GNC
and
/nobackup/lorainelab/data/schallerlab_quickloads/Quickload_Ein3
respectively.
From there Ann can move them to the new chip seq quickload repository.

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Moved unpublished data to new hosting (ask Dr.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:

1. GNC PRJNA435725
2. EIN3 PRJNA185404
3. 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.