Test egapx pipeline

[mpoelchau]

Hi @amcooksey - NCBI has an alpha version out for their eukaryotic annotation pipeline and are looking for feedback. It would be nice if we could test this to see if this could be an option for us in the future. This is not a huge priority now - revisit this issue whenever you have a gap. That said some of the Ag100Pest group are interested in how this goes so it would be great if you could share notes with them.

"Documentation about EGAPx are available on https://github.com/ncbi/egapx, with the egapx.py runner script available from GitHub and all software available in a Docker container for execution using either Docker or Singularity.

EGAPx currently works well for vertebrates and select arthropods (diptera, hymenoptera, lepidoptera, choleoptera), and we'll be adding support for plants and more arthropod orders in the next few months."

Could you:

• do a test run with the example data on Ceres
• Try out the pipeline with:
  • https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_024364675.1/
  • https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_947172395.1/
  • https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_917208135.1/
• Document what resources you allocated + how long it took; any other setup/execution oddities
• TBD: We'd need to compare the output with RefSeq's output. What program we use would probably depend on the extent of the changes. Perhaps https://ccb.jhu.edu/software/stringtie/gffcompare.shtml, or our gff3_merge program.

[amcooksey]

https://docs.google.com/spreadsheets/d/1v12c0igYLgR70waE2cSBtFr7SU6IoHZM0zQXmbGlW9Q/edit#gid=0
contains numbers from runs.

review.md

[amcooksey]

version 0.1.2
-fixed the bug that was causing only 1 chromosome to be annotated
https://docs.google.com/spreadsheets/d/1rNLRE6CFoQ9Eud_9_y6xWTb70tyxZhmxaNkrbZmib7A/edit?gid=573577897#gid=573577897

review_0.1.2.md