utilities/README.md

Dataset maintenance utilities

These are not normally needed to use the dataset! They are only required in special circumstances.

Request all genomes to be fetched from tape archives

This step is not needed unless you are getting errors while the dataset is being downloaded regarding some of the genomes needing to be fetched from tape archives.

$ conda env create --file ../environment.yml
$ conda activate phytozome_genomes_dataset
(phytozome_genomes_dataset) $ ./request_all_genomes.py

Generate fresh genomes table

This should not have to be done to use the dataset. It will use the phytozome_genomes.tsv already in the repository. This will re-query Phytozome for the latest list of genomes.

$ conda env create --file ../environment.yml
$ conda activate phytozome_genomes_dataset
(phytozome_genomes_dataset) $ ./generate_genome_table.py

genomes_unfiltered.tsv will have a mostly filtered list of plant genome FASTA files. Some additional filtering is likely needed to remove any non-genome or redudant FASTAs that slip through.