Update:

• Created new folder H_exemplaris_Z151_Apr_2017 in RENCI hosted directory /projects/igbquickload/lorainelab/www/main/htdocs/rnaseq/
• Added updater script:

  #! /bin/bash
  wget --backups=3 https://bitbucket.org/hotpollen/tardigrade/raw/main/quickload/H_exemplaris_Z151_Apr_2017/annots.xml
  

I will put annots.xml files into bitbucket repository and use the update.sh script to re-deploy meta-data files when required.

Update:

• New quickload configuration is available for review and testing but not yet deployed in the default rna-seq quickload data sources
• I added a README.md file at the top level of https://bitbucket.org/lorainelab/tardigrade with instructions on how to open the QL data sources in IGB. Not yet tested, however. Not ready for review or testing at this time.

Based on verbal confirmation from Paige Kulzer, I think this is ready for testing.

To test:

• Confirm that all files can be loaded

Dylan Marrotte - to test:

• Start IGB 10.0.1
• Select the Hypsibius exemplaris genome
• In the Available Data window of the Data Access tab, look under the RNA-Seq folder for "RNA-Seq analysis of Hybsibius exemplaris under DNA damaging stresses (SRP450893)"
• Select a file (Reads, Graph - Scaled, Junctions), zoom in to any gene, and then click the Load Data button in IGB.
• Check that data load (may need to zoom out a little or find another gene if no data for the gene you chose), and also check that there are no errors in the log.
• Do this for every file.
• Double check that all files located here are in IGB.

I doubled check that all the files located in the link provided in the last bullet point were located in IGB and they were.

All of the Reads and Graph - Scaled files loaded into IGB properly.

However, all of the Junction files did not load when I tried. An error pop up message appeared (attached) whenever I tried to load any of the files from IGB.

Update:

• I had forgotten to create these files.
• Proceeding to make them now: added new code to tardigrade repository in "src" directory including: find junctions script and find junctions Java jar file

Update:

• Launched UNC Charlotte VPN to gain access to UNC Charlotte internal network
• Logged into data deployment site (data.bioviz.org, hosted at UNC Charlotte)
• Changed to data deployment directory's parent directory: /mnt/igbdata/tardigrade/H_exemplaris_Z151_Apr_2017
• Launched tmux session (in case I lose my connection during a potentially lengthy transfer)
• Updated data deployment directory with:

rsync -rtpvz aloraine@10.16.115.245:/projects/tomato_genome/fnb/dataprocessing/tardigrade/SRP450893/for_quickload/H_exemplaris_Z151_Apr_2017/SRP450893/* SRP450893/.

The above command compares the contents (using * file glob) of the source directory (first argument) to the contents of the target directory (second argument). Any files that exist in the source directory get copied to the target directory, preserving time stamp (-t) and permissions (-p).

To check that the transfer was done, I visited this URL:

• https://data.bioviz.org/tardigrade/H_exemplaris_Z151_Apr_2017/SRP450893/ confirms th

I observed there are now "FJ" (find junctions) files present here, whereas before, they were absent.

Ready for re-review by Dylan Marrotte.

Re-review:

Started IGB 10.0.1, selected the Hypsibius exemplaris genome, and looked under the RNA-Seq folder for 'RNA-Seq analysis of Hypsibius exemplaris under DNA damaging stresses (SRP450893)'.

I doubled check that all the files located in the link provided in the last bullet point were located in IGB and they were.

Individually selected each file (Reads, Graph - Scaled, Junctions) and clicked the Load Data button in IGB to check for errors as well as errors in the log.

All files loaded data properly and there were no errors in the log!