prepare and load AGR examples locally

[nathandunn]

For yeast, Ensembl works well:

unrelated, but where can I get your original FASTA and GFF3 files? Are you just grabbing most of them through here? https://uswest.ensembl.org/Saccharomyces_cerevisiae/Info/Index

from @scottcain

For yeast, fly and worm, I got the fastas from the individual MODs' download pages. For zebrafish, mouse, rat and human, I got the fastas from RefSeq (making sure to get the right assemblies!). For the GFFs, I got the URLs from https://fms.alliancegenome.org/api/datafile/by/GFF/ (the url is the "s3path" value appended to http://download.alliancegenome.org/)

• [x] get each GFF3 file
• [x] create a tabix version of each file (easier to store and faster to retrieve if needed)
• [x] get each refseq file
• [x] upload refseq for new genome and tabix GFF3 for each track
• [x] save and upload that resultant temp file (in docker)
• [ ] upload each to https://apollo-jbrowse-data.s3.amazonaws.com/${organism}.tgz

For each organism I need to (a) create a correct JBrowse directory, (b) provide a valid GFF3.

• [x] yeast
• [x] worm
• [x] fly
• [x] fish
• [ ] mouse
• [ ] rat
• [x] human

[nathandunn]

wget fro here: https://s3.console.aws.amazon.com/s3/buckets/apollo-jbrowse-data/?region=us-east-1

[nathandunn]

wget ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.33_FB2020_02/fasta/dmel-all-chromosome-r6.33.fasta.gz