galaxyproject / galaxyproject/training-material

NCBI changed the "latest" assembly location for SARS-Cov-2 genome fasta used in tutorials

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Description

Genome: `NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome`

Top-level dirs, note the timestamps:

* FTP RefSeq: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v2
* FTP Genbank: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3

Problem:
* Correct RefSeq fasta link: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v2/GCF_009858895.2_ASM985889v2_genomic.fna.gz
* Correct Genbank fasta link (identical to RefSeq): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.fna.gz
* What we in tutorials (as of Sunday, produces a 404): https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.gz

Impact:
* At least two GTN tutorials: https://github.com/galaxyproject/training-material/search?q=ASM985889v3
* Other places?

Merged assembly records, see history:
https://www.ncbi.nlm.nih.gov/assembly/GCF_009858895.2/

Test histories:
https://usegalaxy.org/u/jen-galaxyproject/h/test-ngs-logistics-tuto
https://usegalaxy.eu/u/jenj/h/test-ngs-logistics-tuto

ping @mvdbeek Would this touch anything else that needs an update?

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