From dc084de2c650c078f63dab570d5974499f05e655 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Wed, 3 Jul 2024 16:58:00 +0200 Subject: [PATCH 1/3] For presentation From 5327e2db4cf3d95e03179fa6ba0c1fbb67ed913b Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Wed, 3 Jul 2024 19:43:12 +0200 Subject: [PATCH 2/3] Customize --- kubernetes/loculus/values.yaml | 203 +-------------------------------- 1 file changed, 5 insertions(+), 198 deletions(-) diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml index af49e771a..e6ef839dc 100644 --- a/kubernetes/loculus/values.yaml +++ b/kubernetes/loculus/values.yaml @@ -775,65 +775,6 @@ defaultOrganismConfig: &defaultOrganismConfig - name: L sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/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 - ebola-sudan: - <<: *defaultOrganismConfig - schema: - <<: *schema - organismName: "Ebola Sudan" - image: "https://www.nih.gov/sites/default/files/styles/featured_media_breakpoint-medium/public/news-events/news-releases/2023/niaid-03.jpg?itok=m4wFNGkn×tamp=1675437186" - metadataAdd: - - name: total_stop_codons - type: int - header: "Alignment states and QC metrics" - noInput: true - preprocessing: - inputs: {input: nextclade.qc.stopCodons.totalStopCodons} - - name: stop_codons - header: "Alignment states and QC metrics" - noInput: true - preprocessing: - inputs: {input: nextclade.qc.stopCodons.stopCodons} - preprocessing: - - <<: *preprocessing - configFile: - <<: *preprocessingConfigFile - nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/ebola/data_output - nextclade_dataset_name: nextstrain/ebola/sudan - ingest: - <<: *ingest - configFile: - taxon_id: 3052460 - referenceGenomes: - nucleotideSequences: - - name: "main" - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/reference.fasta]]" - genes: - - name: NP - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/NP.fasta]]" - - name: VP35 - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/VP35.fasta]]" - - name: VP40 - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/VP40.fasta]]" - - name: GP - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/GP.fasta]]" - - name: ssGP - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/ssGP.fasta]]" - - name: sGP - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/sGP.fasta]]" - - name: VP30 - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/VP30.fasta]]" - - name: VP24 - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/VP24.fasta]]" - - name: L - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-sudan/L.fasta]]" mpox: <<: *defaultOrganismConfig schema: @@ -901,7 +842,7 @@ defaultOrganisms: configFile: <<: *ingestConfigFile taxon_id: 10244 - subsample_fraction: 0.1 + subsample_fraction: 1.0 referenceGenomes: nucleotideSequences: - name: "main" @@ -909,87 +850,10 @@ defaultOrganisms: genes: - name: OPG001 sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/mpox/OPG001.fasta]]" - west-nile: - <<: *defaultOrganismConfig - schema: - <<: *schema - organismName: "West Nile Virus" - image: "https://upload.wikimedia.org/wikipedia/commons/thumb/1/1e/West_Nile_Virus_Image.jpg/256px-West_Nile_Virus_Image.jpg?20200815184100" - metadataAdd: - - name: lineage - header: "Lineage" - noInput: true - generateIndex: true - autocomplete: true - initiallyVisible: true - preprocessing: - inputs: {input: nextclade.clade} - - name: total_stop_codons - type: int - header: "Alignment states and QC metrics" - noInput: true - preprocessing: - inputs: {input: nextclade.qc.stopCodons.totalStopCodons} - - name: stop_codons - header: "Alignment states and QC metrics" - noInput: true - preprocessing: - inputs: {input: nextclade.qc.stopCodons.stopCodons} - website: - <<: *website - tableColumns: - - sample_collection_date - - ncbi_release_date - - authors - - author_affiliations - - geo_loc_country - - geo_loc_admin_1 - - length - - lineage - defaultOrderBy: sample_collection_date - 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 - referenceGenomes: - nucleotideSequences: - - name: main - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/reference.fasta]]" - genes: - - name: 2K - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/2K.fasta]]" - - name: NS1 - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS1.fasta]]" - - name: NS2A - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS2A.fasta]]" - - name: NS2B - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS2B.fasta]]" - - name: NS3 - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS3.fasta]]" - - name: NS4A - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS4A.fasta]]" - - name: NS4B - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS4B.fasta]]" - - name: NS5 - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS5.fasta]]" - - name: capsid - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/capsid.fasta]]" - - name: env - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/env.fasta]]" - - name: prM - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/prM.fasta]]" - dummy-organism: + sars-cov-2: schema: image: "https://www.un.org/sites/un2.un.org/files/field/image/1583952355.1997.jpg" - organismName: "Test Dummy Organism" + organismName: "SARS-CoV-2" metadata: - name: date type: date @@ -1071,63 +935,6 @@ defaultOrganisms: sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/ORF9b.fasta]]" - name: "S" sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/S.fasta]]" - cchf: - <<: *defaultOrganismConfig - schema: - <<: *schema - organismName: "Crimean-Congo Hemorrhagic Fever Virus" - nucleotideSequences: [L, M, S] - image: "https://upload.wikimedia.org/wikipedia/commons/thumb/5/5e/Crimean-Congo_Hemorrhagic_Fever_%28CCHF%29_Virus_%2840689899455%29.jpg/1920px-Crimean-Congo_Hemorrhagic_Fever_%28CCHF%29_Virus_%2840689899455%29.jpg" - website: - <<: *website - tableColumns: - - sample_collection_date - - geo_loc_country - - geo_loc_admin_1 - - authors - - author_affiliations - - ncbi_release_date - - host_name_scientific - - length_M - - length_S - - length_L - defaultOrderBy: sample_collection_date - 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 - nucleotideSequences: [L, M, S] - genes: [RdRp, GPC, NP] - ingest: - <<: *ingest - configFile: - <<: *ingestConfigFile - taxon_id: 3052518 - nucleotide_sequences: - - L - - M - - S - nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output - nextclade_dataset_name: nextstrain/cchfv/linked - referenceGenomes: - nucleotideSequences: - - name: L - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/reference_L.fasta]]" - - name: M - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/reference_M.fasta]]" - - name: S - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/reference_S.fasta]]" - genes: - - name: RdRp - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/RdRp.fasta]]" - - name: GPC - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/GPC.fasta]]" - - name: NP - sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/NP.fasta]]" auth: smtp: host: "in-v3.mailjet.com" @@ -1192,5 +999,5 @@ enableCrossRefCredentials: true runDevelopmentKeycloakDatabase: true runDevelopmentMainDatabase: true enforceHTTPS: true -registrationTermsMessage: > - You must agree to the terms of use. \ No newline at end of file +registrationTermsMessage: >- + You must agree to the terms of use. From 84dc636cef0f24830a9b5b804f3dbe6bd3fd242b Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Fri, 5 Jul 2024 10:55:07 +0200 Subject: [PATCH 3/3] Switch image --- kubernetes/loculus/values.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml index e6ef839dc..9abe544e4 100644 --- a/kubernetes/loculus/values.yaml +++ b/kubernetes/loculus/values.yaml @@ -852,7 +852,7 @@ defaultOrganisms: sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/mpox/OPG001.fasta]]" sars-cov-2: schema: - image: "https://www.un.org/sites/un2.un.org/files/field/image/1583952355.1997.jpg" + image: "https://raw.githubusercontent.com/corneliusroemer/demo-data/main/sars.webp" organismName: "SARS-CoV-2" metadata: - name: date