Species archetypes 🎃

hugo/config.yaml

@@ -12,6 +12,10 @@ markup:
     endLevel: 4
     ordered: false
 
+module:
+  imports:
+    - path: genome-portal-kit
+
 menus:
   main:
   - name: About

hugo/content/species/cucurbita_pepo/_index.md

@@ -0,0 +1,97 @@
+---
+date: 2024-11-20T16:23:21+01:00
+title: Cucurbita pepo
+subtitle:
+lastmod: 2024-11-20T16:23:21+01:00
+draft: true
+cascade:
+  params:
+    draft: true
+type: species_bundle
+layout: "intro"
+weight: 1
+
+resources:
+- title: 'Cucurbita pepo'
+  name: cover_image
+  src: "pepo.jpg"
+  params:
+    attribution: CC-BY-SA
+    link: "https://placehold.co/600x400/png"
+
+
+lineage: {
+    "clade": {
+      "scientificName": "Embryophyta",
+      "taxId": "3193"
+    },
+    "class": {
+      "scientificName": "Magnoliopsida",
+      "taxId": "3398"
+    },
+    "family": {
+      "scientificName": "Cucurbitaceae",
+      "taxId": "3650"
+    },
+    "genus": {
+      "scientificName": "Cucurbita",
+      "taxId": "3660"
+    },
+    "kingdom": {
+      "scientificName": "Viridiplantae",
+      "taxId": "33090"
+    },
+    "order": {
+      "scientificName": "Cucurbitales",
+      "taxId": "71239"
+    },
+    "phylum": {
+      "scientificName": "Streptophyta",
+      "taxId": "35493"
+    },
+    "species": {
+      "scientificName": "Cucurbita pepo",
+      "taxId": "3663"
+    },
+    "subphylum": {
+      "scientificName": "Streptophytina",
+      "taxId": "131221"
+    },
+    "superkingdom": {
+      "scientificName": "Eukaryota",
+      "taxId": "2759"
+    },
+    "tribe": {
+      "scientificName": "Cucurbiteae",
+      "taxId": "1003878"
+    }
+  }
+# Use this setting to override the default taxonomy ranks to display.
+# See config/_default/params.yaml for the syntax to use.
+taxonomy_ranks:
+params:
+  banner_title: "Species overview"
+  goat_webpage: 'https://goat.genomehubs.org/record?recordId=3663&result=taxon&taxonomy=ncbi'
+
+  # Map
+  gbif_taxon_id: 2874508
+  latitude: 0
+  longitude: 0
+  initialZoom: 1
+
+  # Optional
+  iucn_category:
+  iucn_link:
+  swe_red_list:
+  swe_red_list_link:
+---
+
+### Description
+
+#### Genome reference
+
+#### References
+
+#### Changelog
+
+- Nov 20, 2024 - Species first published on the Portal

hugo/content/species/cucurbita_pepo/assembly/assembly.yaml

@@ -0,0 +1,29 @@
+description:
+  name:
+  type:
+  level:
+  repr:
+  accession:
+stats:
+  length:
+  gc:
+  contig:
+  contig_n50:
+  contig_l50:
+  contig_n90:
+  contig_l90:
+  scaffold:
+  scaffold_n50:
+  scaffold_l50:
+  scaffold_n90:
+  scaffold_l90:
+  scaffold_gt_10:
+  busco:
+annotation:
+  gene_cnt:
+  transcript_cnt:
+  exons_avg:
+  gene_length_avg:
+  transcript_length_avg:
+  exon_length_avg:
+  intron_length_avg:

hugo/content/species/cucurbita_pepo/assembly/contrib.md

@@ -0,0 +1,14 @@
+---
+build:
+  list: never
+  publishResources: false
+  render: never
+---
+<!-- markdownlint-disable first-line-heading -->
+### Contributor(s)
+
+### Publication(s)
+
+### Funding
+
+### Acknowledgements

hugo/content/species/cucurbita_pepo/assembly/index.md

@@ -0,0 +1,8 @@
+---
+title: "Genome assembly"
+type: species_bundle
+layout: assembly
+lastmod: 2024-11-21T10:58:49+01:00
+---
+
+### Methods

hugo/content/species/cucurbita_pepo/download/data_tracks.json

@@ -0,0 +1,16 @@
+[
+  {
+    "dataTrackName": "Genome",
+    "description": "Reference genome sequence",
+    "fileName": "placeholder.fasta.gz",
+    "links": [
+      {"Download": "#"},
+      {"Website": "#"},
+      {"Article": "#"}
+    ],
+    "accessionOrDOI": "GCA_1234",
+    "principalInvestigator": "Someone",
+    "principalInvestigatorAffiliation": "Some university",
+    "firstDateOnPortal": "15 October 2024"
+  }
+]

hugo/content/species/cucurbita_pepo/download/index.md

@@ -0,0 +1,7 @@
+---
+title: "Download"
+type: species_bundle
+layout: download
+weight: 3
+lastmod: 2024-11-21T10:58:49+01:00
+---

hugo/content/species/cucurbita_pepo/lineage.default.yaml

@@ -0,0 +1,35 @@
+# Example lineage configuration.
+# This format is expeced by the .Params.lineage front matter key in `_index.md`
+clade:
+  scientificName: Embryophyta
+  taxId: "3193"
+class:
+  scientificName: Magnoliopsida
+  taxId: "3398"
+family:
+  scientificName: Cucurbitaceae
+  taxId: "3650"
+genus:
+  scientificName: Cucurbita
+  taxId: "3660"
+kingdom:
+  scientificName: Viridiplantae
+  taxId: "33090"
+order:
+  scientificName: Cucurbitales
+  taxId: "71239"
+phylum:
+  scientificName: Streptophyta
+  taxId: "35493"
+species:
+  scientificName: Cucurbita pepo
+  taxId: "3663"
+subphylum:
+  scientificName: Streptophytina
+  taxId: "131221"
+superkingdom:
+  scientificName: Eukaryota
+  taxId: "2759"
+tribe:
+  scientificName: Cucurbiteae
+  taxId: "1003878"

hugo/themes/genome-portal-kit/README.md

@@ -0,0 +1,8 @@
+# Genome portal
+A Hugo theme for a genome portal embedding the JBrowse2 genome browser.
+
+## Features
+
+## Installation
+
+## Configuration

hugo/themes/genome-portal-kit/archetypes/species/_index.md

@@ -0,0 +1,57 @@
+{{- $scientificName := replace .File.ContentBaseName `_` ` ` | strings.FirstUpper -}}
+---
+date: {{ .Date }}
+title: {{ $scientificName }}
+subtitle:
+lastmod: {{ .Date }}
+
+draft: true
+cascade:
+  params:
+    draft: true
+type: species_bundle
+layout: intro
+weight: 1
+
+resources:
+  - title: '{{ $scientificName }}'
+    name: cover_image
+    src: "placeholder.png"
+    params:
+      attribution: CC-BY-SA
+      link: "https://placehold.co/600x400/png"
+
+{{ $taxId := partial "species_bundle/GetTaxId" $scientificName }}
+lineage: {{ partial "species_bundle/LineageConfig" $taxId }}
+# Use this setting to override the default taxonomy ranks to display.
+# See config/_default/params.yaml for the syntax to use.
+taxonomy_ranks:
+params:
+  banner_title: "Species overview"
+  goat_webpage: '{{ printf
+  "https://goat.genomehubs.org/record?recordId=%s&result=taxon&taxonomy=ncbi"
+  $taxId
+  }}'
+
+  # Map
+  gbif_taxon_id: {{ partial "species_bundle/GetGbifKey.html" $scientificName }}
+  latitude: 0
+  longitude: 0
+  initialZoom: 1
+
+  # Optional
+  iucn_category:
+  iucn_link:
+  swe_red_list:
+  swe_red_list_link:
+---
+
+### Description
+
+#### Genome reference
+
+#### References
+
+#### Changelog
+
+- {{ .Date | time.Format ":date_medium" }} - Species first published on the Portal

hugo/themes/genome-portal-kit/archetypes/species/assembly/assembly.yaml

@@ -0,0 +1,29 @@
+description:
+  name:
+  type:
+  level:
+  repr:
+  accession:
+stats:
+  length:
+  gc:
+  contig:
+  contig_n50:
+  contig_l50:
+  contig_n90:
+  contig_l90:
+  scaffold:
+  scaffold_n50:
+  scaffold_l50:
+  scaffold_n90:
+  scaffold_l90:
+  scaffold_gt_10:
+  busco:
+annotation:
+  gene_cnt:
+  transcript_cnt:
+  exons_avg:
+  gene_length_avg:
+  transcript_length_avg:
+  exon_length_avg:
+  intron_length_avg:

hugo/themes/genome-portal-kit/archetypes/species/assembly/contrib.md

@@ -0,0 +1,14 @@
+---
+build:
+  list: never
+  publishResources: false
+  render: never
+---
+<!-- markdownlint-disable first-line-heading -->
+### Contributor(s)
+
+### Publication(s)
+
+### Funding
+
+### Acknowledgements

hugo/themes/genome-portal-kit/archetypes/species/assembly/index.md

@@ -0,0 +1,8 @@
+---
+title: "Genome assembly"
+type: species_bundle
+layout: assembly
+lastmod: {{ .Date }}
+---
+
+### Methods

hugo/themes/genome-portal-kit/archetypes/species/download/data_tracks.json

@@ -0,0 +1,16 @@
+[
+  {
+    "dataTrackName": "Genome",
+    "description": "Reference genome sequence",
+    "fileName": "placeholder.fasta.gz",
+    "links": [
+      {"Download": "#"},
+      {"Website": "#"},
+      {"Article": "#"}
+    ],
+    "accessionOrDOI": "GCA_1234",
+    "principalInvestigator": "Someone",
+    "principalInvestigatorAffiliation": "Some university",
+    "firstDateOnPortal": "15 October 2024"
+  }
+]

hugo/themes/genome-portal-kit/archetypes/species/download/index.md

@@ -0,0 +1,7 @@
+---
+title: "Download"
+type: species_bundle
+layout: download
+weight: 3
+lastmod: {{ .Date }}
+---