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Merge branch 'TASK-7100' of github.com:opencb/jsorolla into TASK-7100
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@imedina
imedina committed Dec 18, 2024
2 parents 06fcdb0 + be6fdd4 commit afa4836
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Showing 14 changed files with 600 additions and 909 deletions.
236 changes: 4 additions & 232 deletions src/sites/iva/conf/config.js
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Original file line number Diff line number Diff line change
Expand Up @@ -188,234 +188,6 @@ const CATALOG_NAVBAR_MENU = {
]
};

const ANALYSIS_TOOLS = {
id: "analysis",
name: "Analysis Tools",
description: "",
menu: [
{
name: "Analysis Execution",
visibility: "public",
submenu: [
{
id: "tool-analysis",
name: "Tool Executor",
description: "",
visibility: "public"
},
{
id: "custom-tool-builder",
name: "Custom Tool Builder",
description: "",
visibility: "public"
},
{
id: "workflow-analysis",
name: "Workflow Executor",
description: "",
visibility: "public"
},
],
},
{
name: "Summary Stats",
visibility: "public",
submenu: [
{
id: "sample-variant-stats",
name: "Sample Variant Stats",
description: "",
visibility: "public"
},
{
id: "cohort-variant-stats",
name: "Cohort Variant Stats",
description: "",
visibility: "public"
},
],
},
{
name: "Association Analysis",
visibility: "public",
submenu: [
{
id: "gwas",
name: "Genome-Wide Association Study (GWAS)",
description: "Study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait",
visibility: "public",
},
],
},
{
name: "Sample Analysis",
visibility: "public",
submenu: [
{
id: "knockout",
name: "Knockout Analysis",
description: "",
visibility: "public"
},
{
id: "sample-eligibility",
name: "Eligibility Analysis",
description: "",
visibility: "public"
},
],
},
{
name: "Individual Analysis",
visibility: "public",
submenu: [
{
id: "inferred-sex",
name: "Sex Inference",
description: "",
visibility: "public"
},
{
id: "individual-relatedness",
name: "Relatedness",
description: "",
visibility: "public"
},
{
id: "mendelian-error",
name: "Mendelian Errors",
description: "",
visibility: "public"
},
],
},
{
name: "Cancer Analysis",
visibility: "public",
submenu: [
{
id: "mutational-signature",
name: "Mutational Signature",
description: "",
visibility: "public"
},
],
},
{
name: "Quality Control",
visibility: "public",
submenu: [
{
id: "sample-qc",
name: "Sample Quality Control",
description: "Calculate different genetic checks and metrics and store data in Sample Catalog",
visibility: "public"
},
{
id: "individual-qc",
name: "Individual Quality Control",
description: "Calculate different genetic checks and metrics and store data in Individual Catalog",
visibility: "public"
},
{
id: "family-qc",
name: "Family Quality Control",
description: "Calculate different genetic checks and metrics and store data in Family Catalog",
visibility: "public"
},
],
},
{
name: "Export",
visibility: "public",
submenu: [
{
id: "variant-export",
name: "Variant Export",
description: `
Filter and export variants, with their annotation and sample genotypes,
from the Variant Storage to a file in multiple supported formats (vcf, json, tped, ensembl vep tab...)
for being shared or processed by an external tool.
`,
visibility: "public"
},
{
id: "variant-stats-exporter",
name: "Variant Stats Export",
description: "Export variant stats for different cohorts",
visibility: "public"
},
],
},
{
name: "External Tools",
visibility: "public",
submenu: [
{
id: "beacon",
name: "GA4GH Beacon",
description: "Find databases that have information about specific variants.",
visibility: "public"
},
{
id: "plink",
name: "Plink",
description: "",
visibility: "public"
},
{
id: "gatk",
name: "GATK",
description: "",
visibility: "public"
},
{
id: "bcftools",
name: "BCFtools",
description: "",
visibility: "public"
},
],
},
{
name: "Data Management",
visibility: "public",
submenu: [
{
id: "alignment-index",
name: "Alignment Index",
description: "Create a .bai index file.",
visibility: "public"
},
{
id: "coverage-index",
name: "Coverage Index",
description: "Precompute coverage in a BigWig file",
visibility: "public"
},
],
},
{
name: "Summary Stats",
visibility: "public",
submenu: [
{
id: "alignment-stats",
name: "Alignment Stats",
description: "Compute BAM stats using samtools",
visibility: "public"
},
{
id: "beacon",
name: "GA4GH Beacon",
description: "Find databases that have information about specific variants.",
visibility: "public"
},
],
},
],
};

const SUITE = {
id: "suite",
name: "OpenCB Suite",
Expand Down Expand Up @@ -492,12 +264,8 @@ const SUITE = {
}
},
welcomePage: {
display: {
titleStyle: "text-align:center"
},
title: "OpenCB Suite",
logo: "img/iva.svg",
bottomLogo: {img: "", link: "", height: ""},
content: `
Welcome to the OpenCB Suite for whole genome variant analysis.
This interactive tool allows finding genes affected by deleterious variants that segregate along family pedigrees, case-controls or sporadic samples.
Expand Down Expand Up @@ -562,6 +330,7 @@ const SUITE = {
title: "Research Environment",
description: "Explore variants in real-time and execute analysis and tools.",
icon: "fa-flask",
color: "#3789FB",
logo: "img/tools/icons/variant_browser_white.svg",
logoAlt: "img/tools/icons/variant_browser.svg",
visibility: "public",
Expand Down Expand Up @@ -650,6 +419,7 @@ const SUITE = {
title: "Clinical Analysis",
description: "Create cases, execute clinical interpretations, and create clinical reports.",
icon: "fa-stethoscope",
color: "#FA8938",
logo: "img/tools/icons/interpretation_portal_white.svg",
logoAlt: "img/tools/icons/interpretation_portal.svg",
visibility: "public",
Expand Down Expand Up @@ -734,6 +504,7 @@ const SUITE = {
title: "Data Catalog",
description: "Manage and explore your data, files, samples, individuals, and families.",
icon: "fa-archive",
color: "#15D0C1",
logo: "img/tools/icons/interpretation_portal_white.svg",
logoAlt: "img/tools/icons/interpretation_portal.svg",
visibility: "public",
Expand Down Expand Up @@ -842,6 +613,7 @@ const SUITE = {
id: "admin",
name: "Admin",
icon: "fa-user-cog",
color: "#9C64F7",
description: "Administration tools for managing users, projects, and studies.",
logo: "img/tools/icons/file_explorer_white.svg",
logoAlt: "img/tools/icons/file_explorer.svg",
Expand Down
4 changes: 1 addition & 3 deletions src/sites/iva/iva-app.js
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Original file line number Diff line number Diff line change
Expand Up @@ -135,7 +135,6 @@ class IvaApp extends LitElement {
_config.consequenceTypes = CONSEQUENCE_TYPES;
_config.populationFrequencies = POPULATION_FREQUENCIES;
_config.proteinSubstitutionScores = PROTEIN_SUBSTITUTION_SCORE.style;
_config.analysisTools = ANALYSIS_TOOLS;

// Reading the default settings from the config files, eg. browser.settings.js
// Store them in a flat structure.
Expand Down Expand Up @@ -1597,8 +1596,7 @@ class IvaApp extends LitElement {
case "analysis-tools":
content = html`
<analysis-tools
.opencgaSession="${this.opencgaSession}"
.config="${this.config.analysisTools}">
.opencgaSession="${this.opencgaSession}">
</analysis-tools>
`;
break;
Expand Down
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