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Check/update READMEs for new Cicer collections #120

Closed sammyjava closed 1 year ago

sammyjava commented 2 years ago

I've uploaded the new Cicer collections to the public DS. Please look over the READMEs and update them as appropriate. In particular, the expression READMEs are basically stubs that I created so that I could load them into CicerMine.

I have NOT added the new species to the genus description file so they should not appear on legumeinfo.org after a rebuild. They should be added when we want the new species collections to appear on the Jekyll website.

I have not added the BUSCO stuff since it is bulky and I don't store it locally. You'll need to upload that stuff if desired.

Cicer
├── arietinum
│   ├── annotations
│   │   ├── CDCFrontier.gnm3.ann1.NPD7
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.NPD7.cds.fna.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.NPD7.gcv_genes.gff3.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.NPD7.gene_models_main.gff3.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.NPD7.legfed_v1_0.M65K.gfa.tsv.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.NPD7.mrna.fna.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.NPD7.protein.faa.gz
│   │   │   └── README.CDCFrontier.gnm3.ann1.NPD7.yml
│   ├── expression
│   │   ├── CDCFrontier.gnm3.ann1.expr.CDC_Consul.Perilla-Henao_2018
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.CDC_Consul.Perilla-Henao_2018.obo.tsv.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.CDC_Consul.Perilla-Henao_2018.samples.tsv.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.CDC_Consul.Perilla-Henao_2018.values.tsv.gz
│   │   │   └── README.CDCFrontier.gnm3.ann1.expr.CDC_Consul.Perilla-Henao_2018.yml
│   │   ├── CDCFrontier.gnm3.ann1.expr.Hybrid.Cook_2018
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.Hybrid.Cook_2018.obo.tsv.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.Hybrid.Cook_2018.samples.tsv.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.Hybrid.Cook_2018.values.tsv.gz
│   │   │   └── README.CDCFrontier.gnm3.ann1.expr.Hybrid.Cook_2018.yml
│   │   ├── CDCFrontier.gnm3.ann1.expr.mixed.Moenga_2018
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.mixed.Moenga_2018.obo.tsv.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.mixed.Moenga_2018.samples.tsv.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.mixed.Moenga_2018.values.tsv.gz
│   │   │   └── README.CDCFrontier.gnm3.ann1.expr.mixed.Moenga_2018.yml
│   │   ├── CDCFrontier.gnm3.ann1.expr.mixed.Sutton_2018a
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.mixed.Sutton_2018a.obo.tsv.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.mixed.Sutton_2018a.samples.tsv.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.mixed.Sutton_2018a.values.tsv.gz
│   │   │   └── README.CDCFrontier.gnm3.ann1.expr.mixed.Sutton_2018a.yml
│   │   ├── CDCFrontier.gnm3.ann1.expr.mixed.Sutton_2018b
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.mixed.Sutton_2018b.obo.tsv.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.mixed.Sutton_2018b.samples.tsv.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.ann1.expr.mixed.Sutton_2018b.values.tsv.gz
│   │   │   └── README.CDCFrontier.gnm3.ann1.expr.mixed.Sutton_2018b.yml
│   ├── genomes
│   │   ├── CDCFrontier.gnm3.QT0P
│   │   │   ├── cicar.CDCFrontier.gnm3.QT0P.gcv_genome.gff3.gz
│   │   │   ├── cicar.CDCFrontier.gnm3.QT0P.genome_main.fna.fai
│   │   │   ├── cicar.CDCFrontier.gnm3.QT0P.genome_main.fna.gz
│   │   │   └── README.CDCFrontier.gnm3.QT0P.yml
├── echinospermum
│   ├── about_this_collection
│   │   └── description_Cicer_echinospermum.yml
│   ├── annotations
│   │   └── S2Drd065.gnm1.ann1.YZ9H
│   │       ├── cicec.S2Drd065.gnm1.ann1.YZ9H.cds.fna.gz
│   │       ├── cicec.S2Drd065.gnm1.ann1.YZ9H.gcv_genes.gff3.gz
│   │       ├── cicec.S2Drd065.gnm1.ann1.YZ9H.gene_models_main.gff3.gz
│   │       ├── cicec.S2Drd065.gnm1.ann1.YZ9H.legfed_v1_0.M65K.gfa.tsv.gz
│   │       ├── cicec.S2Drd065.gnm1.ann1.YZ9H.mrna.fna.gz
│   │       ├── cicec.S2Drd065.gnm1.ann1.YZ9H.protein.faa.gz
│   │       └── README.S2Drd065.gnm1.ann1.YZ9H.yml
│   └── genomes
│       └── S2Drd065.gnm1.R888
│           ├── cicec.S2Drd065.gnm1.R888.genome_main.fna.gz
│           └── README.S2Drd065.gnm1.R888.yml
├── GENUS
│   └── about_this_collection
│       └── description_Cicer.yml
└── reticulatum
    ├── about_this_collection
    │   └── description_Cicer_reticulatum.yml
    ├── annotations
    │   └── Besev079.gnm1.ann1.F01Z
    │       ├── cicre.Besev079.gnm1.ann1.F01Z.cds.fna.gz
    │       ├── cicre.Besev079.gnm1.ann1.F01Z.gcv_genes.gff3.gz
    │       ├── cicre.Besev079.gnm1.ann1.F01Z.gene_models_main.gff3.gz
    │       ├── cicre.Besev079.gnm1.ann1.F01Z.legfed_v1_0.M65K.gfa.tsv.gz
    │       ├── cicre.Besev079.gnm1.ann1.F01Z.mrna.fna.gz
    │       ├── cicre.Besev079.gnm1.ann1.F01Z.protein.faa.gz
    │       └── README.Besev079.gnm1.ann1.F01Z.yml
    └── genomes
        └── Besev079.gnm1.2FZC
            ├── cicre.Besev079.gnm1.2FZC.genome_main.fna.gz
            └── README.Besev079.gnm1.2FZC.yml
sammyjava commented 2 years ago

@adf-ncgr I'll handle fleshing out the README.descriptions with Doug et al.

sammyjava commented 1 year ago

I've got CDCFrontier.gnm3.ann1.expr.mixed.Moenga_2018 from Susan and have re-annoyed the other authors.

sammyjava commented 1 year ago

These are all set now.