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legumeinfo / datastore-specifications

Specifications for directory naming, file naming, file contents in the LIS datastore
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Specify /supplements/ collections #19

Open sammyjava opened 2 years ago

sammyjava commented 2 years ago

These may be catch-alls, but that should at least be stated.

Arachis/hypogaea/supplements/
├── _h5ai.header.html
├── mixed.esm.KNWV
│   ├── CHANGES.mixed.esm.KNWV.txt
│   ├── CHECKSUM.mixed.esm.KNWV.md5
│   ├── MANIFEST.mixed.esm.KNWV.correspondence.yml
│   ├── MANIFEST.mixed.esm.KNWV.descriptions.yml
│   ├── mixed.esm.KNWV.SF01_peanut_core_v14.xlsx
│   ├── mixed.esm.KNWV.SF02_SNPs_whole_Axiom_Arachis2.txt.gz
│   ├── mixed.esm.KNWV.SF03_SNPs_whole_Axiom_Arachis2.vcf.gz
│   ├── mixed.esm.KNWV.SF05_SNPs_w_4_gnm_mrgd.fas.gz
│   ├── mixed.esm.KNWV.SF06_chip_and_genome_samples_v05.xlsx
│   ├── mixed.esm.KNWV.SF07_SNPs_w_4_gnm_mrgd_cen98.fas.gz
│   ├── mixed.esm.KNWV.SF08_SNPs_w_4_gnm_mrgd_cen99.fas.gz
│   ├── mixed.esm.KNWV.SF09_SNPs_w_4_gnm_mrgd_rt3_nh.txt.gz
│   ├── mixed.esm.KNWV.SF10_K5_membership.pdf
│   ├── mixed.esm.KNWV.SF11_K5_cluster_assignment.xlsx
│   ├── mixed.esm.KNWV.SF12_pca_34.pdf
│   ├── mixed.esm.KNWV.SF13_chip_and_genome_GFFs.xlsx
│   ├── mixed.esm.KNWV.SF14_PI497426_pods.jpg
│   ├── mixed.esm.KNWV.SF15_Sipan_neclkace_Donnan_Einstein.jpg
│   └── README.mixed.esm.KNWV.yml
└── Tifrunner.esm.TVDM
    ├── CHANGES.Tifrunner.esm.TVDM.txt
    ├── CHECKSUM.Tifrunner.esm.TVDM.md5
    ├── MANIFEST.Tifrunner.esm.TVDM.correspondence.yml
    ├── MANIFEST.Tifrunner.esm.TVDM.descriptions.yml
    ├── original_readme.txt
    ├── README.Tifrunner.esm.TVDM.yml
    ├── Tifrunner.esm.TVDM.SD1_AB_gene_expression.tar.gz
    ├── Tifrunner.esm.TVDM.SD2_Germplasm_key.xlsx
    ├── Tifrunner.esm.TVDM.SD3_Tifrunner.AB.base_assignment.txt.gz
    ├── Tifrunner.esm.TVDM.SD4_Structure_visualizations.tar.gz
    ├── Tifrunner.esm.TVDM.SD5_ABSNPcounts_WGS_diverse.tar.gz
    ├── Tifrunner.esm.TVDM.SD6_IpaDur_OYflower_Genotypes.xlsx
    ├── Tifrunner.esm.TVDM.SD7_Adur_divergences_from_Asubgen.tar.gz
    ├── Tifrunner.esm.TVDM.SD8_Genetic_maps_and_seqs.tar.gz
    └── Tifrunner.esm.TVDM.SD9_Tifrunner_WGS_density_mapping.tar.gz
Cajanus/cajan/supplements/
├── _h5ai.header.html
└── ICPL87119.bac1.GpKx
    ├── cajca.ICPL87119.bac1.GpKx.library_info.txt
    ├── CHANGES.ICPL87119.bac1.GpKx.txt
    ├── CHECKSUM.ICPL87119.bac1.GpKx.md5
    ├── MANIFEST.ICPL87119.bac1.GpKx.correspondence.yml
    ├── MANIFEST.ICPL87119.bac1.GpKx.descriptions.yml
    └── README.ICPL87119.bac1.GpKx.yml
Glycine/max/supplements/
└── mixed.esm.Phansak_Soonsuwon_2016
    ├── glyma.mixed.esm.Phansak_Soonsuwon_2016.accession_key.txt
    ├── glyma.mixed.esm.Phansak_Soonsuwon_2016.batch_R_commands.tar.gz
    ├── glyma.mixed.esm.Phansak_Soonsuwon_2016.genotype_data.tar.gz
    ├── glyma.mixed.esm.Phansak_Soonsuwon_2016.install_R_R_QTL.txt
    ├── glyma.mixed.esm.Phansak_Soonsuwon_2016.parent_accessions.txt
    ├── glyma.mixed.esm.Phansak_Soonsuwon_2016.SNP_names.txt
    ├── MANIFEST.mixed.esm.Phansak_Soonsuwon_2016.correspondence.yml
    ├── MANIFEST.mixed.esm.Phansak_Soonsuwon_2016.descriptions.yml
    └── README.mixed.esm.Phansak_Soonsuwon_2016.yml
LEGUMES/Fabaceae/supplements/
├── _h5ai.header.html
└── legume.genefam.esm.RDQM
    ├── CHANGES.legume.genefam.esm.RDQM.txt
    ├── CHECKSUM.legume.genefam.esm.RDQM.md5
    ├── legume.genefam.esm.RDQM.SD01_65_hmmalign.tar.gz
    ├── legume.genefam.esm.RDQM.SD02_65_hmmalign_trim2.tar.gz
    ├── legume.genefam.esm.RDQM.SD03_70_trees_combined.tar.gz
    ├── legume.genefam.esm.RDQM.SD04_71_trees_reduced_trees.tar.gz
    ├── legume.genefam.esm.RDQM.SD05_tree_legcyc_and_outgrps7boot_color.nh.txt
    ├── legume.genefam.esm.RDQM.SD06_LPWG_chrom_counts_by_genus3_all_colored.pdf
    ├── legume.genefam.esm.RDQM.SD07_LPWG_chrom_counts_by_genus3.tree.txt
    ├── legume.genefam.esm.RDQM.SD08_quota_dotplots.pdf
    ├── legume.genefam.esm.RDQM.SD09_quota_tables.tar.gz
    ├── legume.genefam.esm.RDQM.ST01_basal_legume_histograms.xlsx
    ├── legume.genefam.esm.RDQM.ST02_species_counts_in_gene_families.xlsx
    ├── legume.genefam.esm.RDQM.ST03_legcyc_genes.xlsx
    ├── legume.genefam.esm.RDQM.ST04_legume_matK_matrix_and_counts_v05.xlsx
    ├── legume.genefam.esm.RDQM.ST05_legume_genome_sizes.xlsx
    ├── MANIFEST.legume.genefam.esm.RDQM.correspondence.yml
    ├── MANIFEST.legume.genefam.esm.RDQM.descriptions.yml
    └── README.legume.genefam.esm.RDQM.yml