galaxyproject · guerler · Dec 5, 2024 · Dec 7, 2024 · Dec 7, 2024 · Dec 7, 2024
diff --git a/packages/jbrowse/.gitignore b/packages/jbrowse/.gitignore
@@ -0,0 +1,6 @@
+node_modules
+.DS_Store
+dist
+dist-ssr
+*.local
+*.tsbuildinfo
diff --git a/packages/jbrowse/README.md b/packages/jbrowse/README.md
@@ -0,0 +1,21 @@
+# vite with @jbrowse/react-app
+
+This is a demo of using the @jbrowse/react-app NPM package with vite (see
+https://vitejs.dev/)
+
+Vite is a build system that is very fast and becoming more popular, using
+esbuild and rollup instead of webpack
+
+This particular demo includes several polyfills that are needed for JBrowse
+including the Buffer polyfill
+
+## Demo of `@jbrowse/react-app` with vite
+
+See this app running at https://jbrowse.org/demos/app-vite/.
+
+## Usage
+
+Run `yarn` and then `yarn dev` to start a development instance
+
+Run `yarn build` which produces a `build` directory that can be deployed to a
+static web server
diff --git a/packages/jbrowse/eslint.config.js b/packages/jbrowse/eslint.config.js
@@ -0,0 +1,25 @@
+import js from "@eslint/js";
+import globals from "globals";
+import reactHooks from "eslint-plugin-react-hooks";
+import reactRefresh from "eslint-plugin-react-refresh";
+import tseslint from "typescript-eslint";
+
+export default tseslint.config(
+    { ignores: ["dist"] },
+    {
+        extends: [js.configs.recommended, ...tseslint.configs.recommended],
+        files: ["**/*.{ts,tsx}"],
+        languageOptions: {
+            ecmaVersion: 2020,
+            globals: globals.browser,
+        },
+        plugins: {
+            "react-hooks": reactHooks,
+            "react-refresh": reactRefresh,
+        },
+        rules: {
+            ...reactHooks.configs.recommended.rules,
+            "react-refresh/only-export-components": ["warn", { allowConstantExport: true }],
+        },
+    },
+);
diff --git a/packages/jbrowse/index.html b/packages/jbrowse/index.html
@@ -0,0 +1,11 @@
+<!doctype html>
+<html lang="en">
+  <head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  </head>
+  <body>
+    <div id="app"></div>
+    <script type="module" src="/src/main.js"></script>
+  </body>
+</html>
diff --git a/packages/jbrowse/package.json b/packages/jbrowse/package.json
@@ -0,0 +1,41 @@
+{
+    "name": "galaxy-jbrowse",
+    "type": "module",
+    "version": "0.0.0",
+    "license": "MIT",
+    "scripts": {
+        "dev": "vite",
+        "build": "tsc -b && vite build",
+        "preview": "vite preview",
+        "prettier": "prettier --config ./prettier.config.js --write '**/*.{css,json,js,jsx,ts,tsx,vue}'",
+        "predeploy": "npm run build",
+        "lint": "eslint ."
+    },
+    "devDependencies": {
+        "@eslint/js": "^9.13.0",
+        "@fontsource/roboto": "^5.0.2",
+        "@jbrowse/core": "^2.17.0",
+        "@jbrowse/react-app": "^2.17.0",
+        "@jbrowse/react-linear-genome-view": "^2.17.0",
+        "@types/react": "^18.2.43",
+        "@types/react-dom": "^18.0.9",
+        "@vitejs/plugin-react": "^4.2.1",
+        "@vitejs/plugin-vue": "^5.2.1",
+        "buffer": "^6.0.3",
+        "eslint": "^9.13.0",
+        "eslint-plugin-react-hooks": "^5.0.0",
+        "eslint-plugin-react-refresh": "^0.4.14",
+        "galaxy-charts": "^0.0.40",
+        "galaxy-charts-xml-parser": "^1.0.3",
+        "globals": "^15.11.0",
+        "prettier": "^3.4.2",
+        "react": "^18.0.0",
+        "react-dom": "^18.0.0",
+        "typescript": "^5.3.3",
+        "typescript-eslint": "^8.11.0",
+        "vite": "^5.0.7"
+    },
+    "resolutions": {
+        "@mui/icons-material": "6.0.2"
+    }
+}
diff --git a/packages/jbrowse/prettier.config.js b/packages/jbrowse/prettier.config.js
@@ -0,0 +1,5 @@
+export default {
+    tabWidth: 4,
+    printWidth: 120,
+    bracketSameLine: true,
+};
diff --git a/packages/jbrowse/public/jbrowse.json b/packages/jbrowse/public/jbrowse.json
@@ -0,0 +1,269 @@
+{
+    "assemblies": [
+        {
+            "name": "GRCh38",
+            "aliases": ["hg38"],
+            "sequence": {
+                "type": "ReferenceSequenceTrack",
+                "trackId": "GRCh38-ReferenceSequenceTrack",
+                "adapter": {
+                    "type": "BgzipFastaAdapter",
+                    "fastaLocation": {
+                        "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz"
+                    },
+                    "faiLocation": {
+                        "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai"
+                    },
+                    "gziLocation": {
+                        "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi"
+                    }
+                }
+            },
+            "refNameAliases": {
+                "adapter": {
+                    "type": "RefNameAliasAdapter",
+                    "location": {
+                        "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt"
+                    }
+                }
+            }
+        }
+    ],
+    "tracks": [
+        {
+            "type": "FeatureTrack",
+            "trackId": "genes",
+            "name": "NCBI RefSeq Genes",
+            "assemblyNames": ["GRCh38"],
+            "category": ["Genes"],
+            "adapter": {
+                "type": "Gff3TabixAdapter",
+                "gffGzLocation": {
+                    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz"
+                },
+                "index": {
+                    "location": {
+                        "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.tbi"
+                    }
+                }
+            },
+            "textSearching": {
+                "textSearchAdapter": {
+                    "type": "TrixTextSearchAdapter",
+                    "textSearchAdapterId": "gff3tabix_genes-index",
+                    "ixFilePath": {
+                        "uri": "https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix"
+                    },
+                    "ixxFilePath": {
+                        "uri": "https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ixx"
+                    },
+                    "metaFilePath": {
+                        "uri": "https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz_meta.json"
+                    },
+                    "assemblyNames": ["GRCh38"]
+                }
+            }
+        },
+        {
+            "type": "FeatureTrack",
+            "trackId": "repeats_hg38",
+            "name": "Repeats",
+            "assemblyNames": ["hg38"],
+            "category": ["Annotation"],
+            "adapter": {
+                "type": "BigBedAdapter",
+                "bigBedLocation": {
+                    "uri": "https://jbrowse.org/genomes/GRCh38/repeats.bb",
+                    "locationType": "UriLocation"
+                }
+            }
+        },
+        {
+            "type": "AlignmentsTrack",
+            "trackId": "NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome",
+            "name": "NA12878 Exome",
+            "assemblyNames": ["GRCh38"],
+            "category": ["1000 Genomes", "Alignments"],
+            "adapter": {
+                "type": "CramAdapter",
+                "cramLocation": {
+                    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram"
+                },
+                "craiLocation": {
+                    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram.crai"
+                },
+                "sequenceAdapter": {
+                    "type": "BgzipFastaAdapter",
+                    "fastaLocation": {
+                        "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz"
+                    },
+                    "faiLocation": {
+                        "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai"
+                    },
+                    "gziLocation": {
+                        "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi"
+                    }
+                }
+            }
+        },
+        {
+            "type": "VariantTrack",
+            "trackId": "ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf",
+            "name": "1000 Genomes Variant Calls",
+            "assemblyNames": ["GRCh38"],
+            "category": ["1000 Genomes", "Variants"],
+            "adapter": {
+                "type": "VcfTabixAdapter",
+                "vcfGzLocation": {
+                    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz"
+                },
+                "index": {
+                    "location": {
+                        "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz.tbi"
+                    }
+                }
+            }
+        },
+        {
+            "type": "QuantitativeTrack",
+            "trackId": "hg38.100way.phyloP100way",
+            "name": "hg38.100way.phyloP100way",
+            "category": ["Conservation"],
+            "assemblyNames": ["hg38"],
+            "adapter": {
+                "type": "BigWigAdapter",
+                "bigWigLocation": {
+                    "uri": "https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phyloP100way/hg38.phyloP100way.bw",
+                    "locationType": "UriLocation"
+                }
+            }
+        }
+    ],
+    "defaultSession": {
+        "name": "this session",
+        "margin": 0,
+        "views": [
+            {
+                "id": "linearGenomeView",
+                "minimized": false,
+                "type": "LinearGenomeView",
+                "offsetPx": 191980240,
+                "bpPerPx": 0.1554251851851852,
+                "displayedRegions": [
+                    {
+                        "refName": "10",
+                        "start": 0,
+                        "end": 133797422,
+                        "reversed": false,
+                        "assemblyName": "GRCh38"
+                    }
+                ],
+                "tracks": [
+                    {
+                        "id": "4aZAiE-A3",
+                        "type": "ReferenceSequenceTrack",
+                        "configuration": "GRCh38-ReferenceSequenceTrack",
+                        "minimized": false,
+                        "displays": [
+                            {
+                                "id": "AD3gqvG0_6",
+                                "type": "LinearReferenceSequenceDisplay",
+                                "height": 180,
+                                "configuration": "GRCh38-ReferenceSequenceTrack-LinearReferenceSequenceDisplay",
+                                "showForward": true,
+                                "showReverse": true,
+                                "showTranslation": true
+                            }
+                        ]
+                    },
+                    {
+                        "id": "T6uhrtY40O",
+                        "type": "AlignmentsTrack",
+                        "configuration": "NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome",
+                        "minimized": false,
+                        "displays": [
+                            {
+                                "id": "FinKswChSr",
+                                "type": "LinearAlignmentsDisplay",
+                                "PileupDisplay": {
+                                    "id": "YAAaF494z",
+                                    "type": "LinearPileupDisplay",
+                                    "height": 134,
+                                    "configuration": {
+                                        "type": "LinearPileupDisplay",
+                                        "displayId": "NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_LinearPileupDisplay_xyz"
+                                    },
+                                    "showSoftClipping": false,
+                                    "filterBy": {
+                                        "flagInclude": 0,
+                                        "flagExclude": 1540
+                                    }
+                                },
+                                "SNPCoverageDisplay": {
+                                    "id": "VTQ_VGbAVJ",
+                                    "type": "LinearSNPCoverageDisplay",
+                                    "height": 45,
+                                    "configuration": {
+                                        "type": "LinearSNPCoverageDisplay",
+                                        "displayId": "NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay_snpcoverage_xyz"
+                                    },
+                                    "selectedRendering": "",
+                                    "resolution": 1,
+                                    "constraints": {},
+                                    "filterBy": {
+                                        "flagInclude": 0,
+                                        "flagExclude": 1540
+                                    }
+                                },
+                                "snpCovHeight": 45,
+                                "configuration": "NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome-LinearAlignmentsDisplay",
+                                "height": 179,
+                                "lowerPanelType": "LinearPileupDisplay"
+                            }
+                        ]
+                    },
+                    {
+                        "id": "EUnTnpVI6",
+                        "type": "QuantitativeTrack",
+                        "configuration": "hg38.100way.phyloP100way",
+                        "minimized": false,
+                        "displays": [
+                            {
+                                "id": "mrlawr9Wtg",
+                                "type": "LinearWiggleDisplay",
+                                "height": 100,
+                                "configuration": "hg38.100way.phyloP100way-LinearWiggleDisplay",
+                                "selectedRendering": "",
+                                "resolution": 1,
+                                "constraints": {}
+                            }
+                        ]
+                    },
+                    {
+                        "id": "Cbnwl72EX",
+                        "type": "VariantTrack",
+                        "configuration": "ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf",
+                        "minimized": false,
+                        "displays": [
+                            {
+                                "id": "dvXz01Wf6w",
+                                "type": "LinearVariantDisplay",
+                                "height": 100,
+                                "configuration": "ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf-LinearVariantDisplay"
+                            }
+                        ]
+                    }
+                ],
+                "hideHeader": false,
+                "hideHeaderOverview": false,
+                "hideNoTracksActive": false,
+                "trackSelectorType": "hierarchical",
+                "trackLabels": "overlapping",
+                "showCenterLine": false,
+                "showCytobandsSetting": true,
+                "showGridlines": true,
+                "showTopMenu": false
+            }
+        ]
+    }
+}