Minimal deployment

loculus-project · Nov 19, 2024 · ffd3270 · ffd3270
1 parent 844b49a
commit ffd3270
Showing 1 changed file with 0 additions and 169 deletions.
diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -1136,97 +1136,6 @@ defaultOrganismConfig: &defaultOrganismConfig
       - name: L
         sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-zaire/L.fasta]]"
 defaultOrganisms:
-  ebola-zaire:
-    <<: *defaultOrganismConfig
-    preprocessing:
-      - <<: *preprocessing
-        configFile:
-          <<: *preprocessingConfigFile
-          nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/ebola/data_output
-          nextclade_dataset_name: nextstrain/ebola/zaire
-  west-nile:
-    <<: *defaultOrganismConfig
-    schema:
-      <<: *schema
-      organismName: "West Nile Virus"
-      image: "/images/organisms/wnv_small.jpg"
-      metadataAdd:
-        - name: lineage
-          header: "Lineage"
-          noInput: true
-          generateIndex: true
-          autocomplete: true
-          initiallyVisible: true
-          preprocessing:
-            inputs: {input: nextclade.clade}
-        - name: totalStopCodons
-          type: int
-          header: "Alignment states and QC metrics"
-          noInput: true
-          preprocessing:
-            inputs: {input: nextclade.qc.stopCodons.totalStopCodons}
-        - name: stopCodons
-          header: "Alignment states and QC metrics"
-          noInput: true
-          preprocessing:
-            inputs: {input: nextclade.qc.stopCodons.stopCodons}
-      website:
-        <<: *website
-        tableColumns:
-          - sampleCollectionDate
-          - ncbiReleaseDate
-          - authors
-          - authorAffiliations
-          - geoLocCountry
-          - geoLocAdmin1
-          - length
-          - lineage
-        defaultOrderBy: sampleCollectionDate
-        defaultOrder: descending
-    preprocessing:
-      - <<: *preprocessing
-        configFile:
-          <<: *preprocessingConfigFile
-          nextclade_dataset_name: nextstrain/wnv/all-lineages
-          nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/wnv/data_output
-          genes: [capsid, prM, env, NS1, NS2A, NS2B, NS3, NS4A, 2K, NS4B, NS5]
-    ingest:
-      <<: *ingest
-      configFile:
-        taxon_id: 3048448
-    enaDeposition:
-      configFile:
-        taxon_id: 11082
-        scientific_name: "West Nile virus"
-        molecule_type: "genomic RNA"
-    referenceGenomes:
-      nucleotideSequences:
-        - name: main
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/reference.fasta]]"
-          insdcAccessionFull: NC_009942.1
-      genes:
-        - name: 2K
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/2K.fasta]]"
-        - name: NS1
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/NS1.fasta]]"
-        - name: NS2A
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/NS2A.fasta]]"
-        - name: NS2B
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/NS2B.fasta]]"
-        - name: NS3
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/NS3.fasta]]"
-        - name: NS4A
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/NS4A.fasta]]"
-        - name: NS4B
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/NS4B.fasta]]"
-        - name: NS5
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/NS5.fasta]]"
-        - name: capsid
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/capsid.fasta]]"
-        - name: env
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/env.fasta]]"
-        - name: prM
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/prM.fasta]]"
   dummy-organism:
     schema:
       image: "https://www.un.org/sites/un2.un.org/files/field/image/1583952355.1997.jpg"
@@ -1371,84 +1280,6 @@ defaultOrganisms:
         - name: "main"
           sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/reference.fasta]]"
       genes: []
-  cchf:
-    <<: *defaultOrganismConfig
-    schema:
-      <<: *schema
-      organismName: "Crimean-Congo Hemorrhagic Fever Virus"
-      nucleotideSequences: [L, M, S]
-      image: "/images/organisms/cchf_small.jpg"
-      metadataAdd:
-        - name: hostNameScientific
-          generateIndex: true
-          autocomplete: true
-          header: "Host"
-          ingest: ncbiHostName
-          initiallyVisible: true
-        - name: totalStopCodons
-          type: int
-          header: "Alignment states and QC metrics"
-          noInput: true
-          preprocessing:
-            inputs: {input: nextclade.qc.stopCodons.totalStopCodons}
-        - name: stopCodons
-          header: "Alignment states and QC metrics"
-          noInput: true
-          preprocessing:
-            inputs: {input: nextclade.qc.stopCodons.stopCodons}
-      website:
-        <<: *website
-        tableColumns:
-          - sampleCollectionDate
-          - geoLocCountry
-          - geoLocAdmin1
-          - authors
-          - authorAffiliations
-          - ncbiReleaseDate
-          - hostNameScientific
-          - length_M
-          - length_S
-          - length_L
-        defaultOrderBy: sampleCollectionDate
-        defaultOrder: descending
-    preprocessing:
-      - <<: *preprocessing
-        configFile:
-          <<: *preprocessingConfigFile
-          log_level: DEBUG
-          nextclade_dataset_name: nextstrain/cchfv/linked
-          nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output
-          genes: [RdRp, GPC, NP]
-    ingest:
-      <<: *ingest
-      configFile:
-        <<: *ingestConfigFile
-        taxon_id: 3052518
-        nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output
-        nextclade_dataset_name: nextstrain/cchfv/linked
-    enaDeposition:
-      configFile:
-        taxon_id: 3052518
-        scientific_name: "Orthonairovirus haemorrhagiae"
-        molecule_type: "genomic RNA"
-    referenceGenomes:
-      nucleotideSequences:
-        - name: L
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/reference_L.fasta]]"
-          insdcAccessionFull: NC_005301.3
-        - name: M
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/reference_M.fasta]]"
-          insdcAccessionFull: NC_005300.2
-        - name: S
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/reference_S.fasta]]"
-          insdcAccessionFull: NC_005302.1
-      genes:
-        - name: RdRp
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/RdRp.fasta]]"
-        - name: GPC
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/GPC.fasta]]"
-        - name: NP
-          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/NP.fasta]]"
 auth:
   smtp:
     host: "in-v3.mailjet.com"