IPVC-2379: add necessary NCBI input files to download config

[bsgiles73]

This PR:

• Moves the paths to needed NCBI files to it's own config
• Added the missing files and other genome builds
• Updates download-ncbi script to pull paths from config file
• Updates docker-compose.yml to pass config file parameter

To test these changes I performed the following...

docker build --target uta -t uta-update .

mkdir ncbi

export UTA_ETL_NCBI_DIR=./ncbi

docker compose run ncbi-download

docker compose output...

Downloading files to /ncbi-dir
Downloading ftp.ncbi.nlm.nih.gov::gene/DATA/gene2refseq.gz to /ncbi-dir/gene
receiving incremental file list
DATA/
DATA/gene2refseq.gz
  1,700,651,030 100%   12.73MB/s    0:02:07 (xfr#1, to-chk=0/2)

sent 51 bytes  received 1,701,066,362 bytes  13,034,991.67 bytes/sec
total size is 1,700,651,030  speedup is 1.00
Downloading ftp.ncbi.nlm.nih.gov::gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz to /ncbi-dir/gene
receiving incremental file list
DATA/
DATA/GENE_INFO/
DATA/GENE_INFO/Mammalia/
DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz
      5,120,527 100%    4.81MB/s    0:00:01 (xfr#1, to-chk=0/4)

sent 59 bytes  received 5,121,994 bytes  1,138,234.00 bytes/sec
total size is 5,120,527  speedup is 1.00
...

The resulting output took 8.8Gb of disk space and in the output directory had the following structure...

sgiles-MD6M:uta shane.giles$ tree ncbi
ncbi
├── gene
│   └── DATA
│       ├── GENE_INFO
│       │   └── Mammalia
│       │       └── Homo_sapiens.gene_info.gz
│       └── gene2refseq.gz
├── genomes
│   └── refseq
│       └── vertebrate_mammalian
│           └── Homo_sapiens
│               └── all_assembly_versions
│                   ├── GCF_000001405.25_GRCh37.p13
│                   │   ├── GCF_000001405.25_GRCh37.p13_assembly_report.txt
│                   │   ├── GCF_000001405.25_GRCh37.p13_genomic.fna.gz
│                   │   └── GCF_000001405.25_GRCh37.p13_genomic.gff.gz
│                   ├── GCF_000001405.40_GRCh38.p14
│                   │   ├── GCF_000001405.40_GRCh38.p14_assembly_report.txt
│                   │   ├── GCF_000001405.40_GRCh38.p14_genomic.fna.gz
│                   │   └── GCF_000001405.40_GRCh38.p14_genomic.gff.gz
│                   └── GCF_009914755.1_T2T-CHM13v2.0
│                       ├── GCF_009914755.1_T2T-CHM13v2.0_assembly_report.txt
│                       ├── GCF_009914755.1_T2T-CHM13v2.0_genomic.fna.gz
│                       └── GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz
└── refseq
    └── H_sapiens
        └── mRNA_Prot
            ├── human.1.protein.faa.gz
            ├── human.1.rna.fna.gz
            ├── human.1.rna.gbff.gz
            ├── human.10.protein.faa.gz
            ├── human.10.rna.fna.gz
            ├── human.10.rna.gbff.gz
            ├── human.11.protein.faa.gz
            ├── human.11.rna.fna.gz
            ├── human.11.rna.gbff.gz
...

UPDATE
I verified that if a file is not found by rsync, the script exits with an error code.

Downloading ftp.ncbi.nlm.nih.gov::genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.40_GRCh38.p14/RefSeq_historical_alignments/GCF_000001405.40-RS_2023_03_knownrefseq_alns.gff.gz to /ncbi-dir/genomes
receiving incremental file list
rsync: link_stat "/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.40_GRCh38.p14/RefSeq_historical_alignments/GCF_000001405.40-RS_2023_03_knownrefseq_alns.gff.gz" (in genomes) failed: No such file or directory (2)

sent 8 bytes  received 262 bytes  108.00 bytes/sec
total size is 0  speedup is 0.00
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1865) [Receiver=3.2.7]