Mercurial > repos > fubar > jbrowse2dev
comparison jbrowse2/clienttest.jbrowse @ 6:88b9b105c09b draft
Uploaded
| author | fubar |
|---|---|
| date | Fri, 05 Jan 2024 01:58:02 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 5:42ca8804cd93 | 6:88b9b105c09b |
|---|---|
| 1 { | |
| 2 "configuration": { | |
| 3 "rpc": { | |
| 4 "defaultDriver": "WebWorkerRpcDriver", | |
| 5 "drivers": { | |
| 6 "MainThreadRpcDriver": {}, | |
| 7 "WebWorkerRpcDriver": {} | |
| 8 } | |
| 9 }, | |
| 10 "logoPath": { | |
| 11 "locationType": "UriLocation", | |
| 12 "uri": "" | |
| 13 } | |
| 14 }, | |
| 15 "plugins": [], | |
| 16 "assemblies": [ | |
| 17 { | |
| 18 "name": "Merlin", | |
| 19 "sequence": { | |
| 20 "type": "ReferenceSequenceTrack", | |
| 21 "trackId": "Merlin-1704349310829", | |
| 22 "adapter": { | |
| 23 "type": "IndexedFastaAdapter", | |
| 24 "fastaLocation": { | |
| 25 "locationType": "LocalPathLocation", | |
| 26 "localPath": "/home/ross/rossgit/tools-iuc/tools/jbrowse2/test-data/merlin.fa" | |
| 27 }, | |
| 28 "faiLocation": { | |
| 29 "locationType": "LocalPathLocation", | |
| 30 "localPath": "/tmp/complete/Merlin.fasta.fai" | |
| 31 }, | |
| 32 "metadataLocation": { | |
| 33 "locationType": "UriLocation", | |
| 34 "uri": "/path/to/fa.metadata.yaml" | |
| 35 } | |
| 36 }, | |
| 37 "displays": [ | |
| 38 { | |
| 39 "type": "LinearReferenceSequenceDisplay", | |
| 40 "displayId": "Merlin-1704349310829-LinearReferenceSequenceDisplay" | |
| 41 }, | |
| 42 { | |
| 43 "type": "LinearGCContentDisplay", | |
| 44 "displayId": "Merlin-1704349310829-LinearGCContentDisplay" | |
| 45 } | |
| 46 ] | |
| 47 } | |
| 48 } | |
| 49 ], | |
| 50 "tracks": [ | |
| 51 { | |
| 52 "type": "FeatureTrack", | |
| 53 "trackId": "3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz-1704349390805", | |
| 54 "name": "3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz", | |
| 55 "assemblyNames": [ | |
| 56 "Merlin" | |
| 57 ], | |
| 58 "adapter": { | |
| 59 "type": "BedTabixAdapter", | |
| 60 "bedGzLocation": { | |
| 61 "locationType": "LocalPathLocation", | |
| 62 "localPath": "/tmp/complete/3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz" | |
| 63 }, | |
| 64 "index": { | |
| 65 "location": { | |
| 66 "locationType": "LocalPathLocation", | |
| 67 "localPath": "/tmp/complete/3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz.tbi" | |
| 68 } | |
| 69 } | |
| 70 }, | |
| 71 "displays": [ | |
| 72 { | |
| 73 "type": "LinearBasicDisplay", | |
| 74 "displayId": "3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz-1704349390805-LinearBasicDisplay" | |
| 75 }, | |
| 76 { | |
| 77 "type": "LinearArcDisplay", | |
| 78 "displayId": "3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz-1704349390805-LinearArcDisplay" | |
| 79 } | |
| 80 ] | |
| 81 }, | |
| 82 { | |
| 83 "type": "VariantTrack", | |
| 84 "trackId": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277", | |
| 85 "name": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz", | |
| 86 "assemblyNames": [ | |
| 87 "Merlin" | |
| 88 ], | |
| 89 "adapter": { | |
| 90 "type": "VcfTabixAdapter", | |
| 91 "vcfGzLocation": { | |
| 92 "locationType": "LocalPathLocation", | |
| 93 "localPath": "/tmp/complete/8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz" | |
| 94 }, | |
| 95 "index": { | |
| 96 "location": { | |
| 97 "locationType": "LocalPathLocation", | |
| 98 "localPath": "/tmp/complete/8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz.tbi" | |
| 99 } | |
| 100 } | |
| 101 }, | |
| 102 "textSearching": { | |
| 103 "textSearchAdapter": { | |
| 104 "type": "TrixTextSearchAdapter", | |
| 105 "textSearchAdapterId": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-index", | |
| 106 "ixFilePath": { | |
| 107 "locationType": "LocalPathLocation", | |
| 108 "localPath": "/home/ross/.config/@jbrowse/desktop/autosaved/trix/8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-index.ix" | |
| 109 }, | |
| 110 "ixxFilePath": { | |
| 111 "locationType": "LocalPathLocation", | |
| 112 "localPath": "/home/ross/.config/@jbrowse/desktop/autosaved/trix/8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-index.ixx" | |
| 113 }, | |
| 114 "metaFilePath": { | |
| 115 "locationType": "LocalPathLocation", | |
| 116 "localPath": "/home/ross/.config/@jbrowse/desktop/autosaved/trix/8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-index.json" | |
| 117 }, | |
| 118 "tracks": [ | |
| 119 "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277" | |
| 120 ], | |
| 121 "assemblyNames": [ | |
| 122 "Merlin" | |
| 123 ] | |
| 124 } | |
| 125 }, | |
| 126 "displays": [ | |
| 127 { | |
| 128 "type": "LinearVariantDisplay", | |
| 129 "displayId": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-LinearVariantDisplay" | |
| 130 }, | |
| 131 { | |
| 132 "type": "ChordVariantDisplay", | |
| 133 "displayId": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-ChordVariantDisplay" | |
| 134 }, | |
| 135 { | |
| 136 "type": "LinearPairedArcDisplay", | |
| 137 "displayId": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-LinearPairedArcDisplay" | |
| 138 } | |
| 139 ] | |
| 140 }, | |
| 141 { | |
| 142 "type": "AlignmentsTrack", | |
| 143 "trackId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556", | |
| 144 "name": "859509e7a79c8f48992e130a2a79b36e_0.bam", | |
| 145 "assemblyNames": [ | |
| 146 "Merlin" | |
| 147 ], | |
| 148 "adapter": { | |
| 149 "type": "BamAdapter", | |
| 150 "bamLocation": { | |
| 151 "locationType": "LocalPathLocation", | |
| 152 "localPath": "/tmp/complete/859509e7a79c8f48992e130a2a79b36e_0.bam" | |
| 153 }, | |
| 154 "index": { | |
| 155 "location": { | |
| 156 "locationType": "LocalPathLocation", | |
| 157 "localPath": "/tmp/complete/859509e7a79c8f48992e130a2a79b36e_0.bam.bai" | |
| 158 } | |
| 159 }, | |
| 160 "sequenceAdapter": { | |
| 161 "type": "IndexedFastaAdapter", | |
| 162 "fastaLocation": { | |
| 163 "locationType": "LocalPathLocation", | |
| 164 "localPath": "/home/ross/rossgit/tools-iuc/tools/jbrowse2/test-data/merlin.fa" | |
| 165 }, | |
| 166 "faiLocation": { | |
| 167 "locationType": "LocalPathLocation", | |
| 168 "localPath": "/tmp/complete/Merlin.fasta.fai" | |
| 169 }, | |
| 170 "metadataLocation": { | |
| 171 "locationType": "UriLocation", | |
| 172 "uri": "/path/to/fa.metadata.yaml" | |
| 173 } | |
| 174 } | |
| 175 }, | |
| 176 "displays": [ | |
| 177 { | |
| 178 "type": "LinearAlignmentsDisplay", | |
| 179 "displayId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearAlignmentsDisplay" | |
| 180 }, | |
| 181 { | |
| 182 "type": "LinearPileupDisplay", | |
| 183 "displayId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearPileupDisplay" | |
| 184 }, | |
| 185 { | |
| 186 "type": "LinearSNPCoverageDisplay", | |
| 187 "displayId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearSNPCoverageDisplay" | |
| 188 }, | |
| 189 { | |
| 190 "type": "LinearReadArcsDisplay", | |
| 191 "displayId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearReadArcsDisplay" | |
| 192 }, | |
| 193 { | |
| 194 "type": "LinearReadCloudDisplay", | |
| 195 "displayId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearReadCloudDisplay" | |
| 196 } | |
| 197 ] | |
| 198 }, | |
| 199 { | |
| 200 "type": "FeatureTrack", | |
| 201 "trackId": "1838188642fecd9922f419a0e735e755_0.gff3.gz-1704349668492", | |
| 202 "name": "1838188642fecd9922f419a0e735e755_0.gff3.gz", | |
| 203 "assemblyNames": [ | |
| 204 "Merlin" | |
| 205 ], | |
| 206 "adapter": { | |
| 207 "type": "Gff3TabixAdapter", | |
| 208 "gffGzLocation": { | |
| 209 "locationType": "LocalPathLocation", | |
| 210 "localPath": "/tmp/complete/1838188642fecd9922f419a0e735e755_0.gff3.gz" | |
| 211 }, | |
| 212 "index": { | |
| 213 "location": { | |
| 214 "locationType": "LocalPathLocation", | |
| 215 "localPath": "/tmp/complete/1838188642fecd9922f419a0e735e755_0.gff3.gz.tbi" | |
| 216 } | |
| 217 } | |
| 218 }, | |
| 219 "displays": [ | |
| 220 { | |
| 221 "type": "LinearBasicDisplay", | |
| 222 "displayId": "1838188642fecd9922f419a0e735e755_0.gff3.gz-1704349668492-LinearBasicDisplay" | |
| 223 }, | |
| 224 { | |
| 225 "type": "LinearArcDisplay", | |
| 226 "displayId": "1838188642fecd9922f419a0e735e755_0.gff3.gz-1704349668492-LinearArcDisplay" | |
| 227 } | |
| 228 ] | |
| 229 }, | |
| 230 { | |
| 231 "type": "QuantitativeTrack", | |
| 232 "trackId": "merlin.bw-1704349777260", | |
| 233 "name": "merlin.bw", | |
| 234 "assemblyNames": [ | |
| 235 "Merlin" | |
| 236 ], | |
| 237 "adapter": { | |
| 238 "type": "BigWigAdapter", | |
| 239 "bigWigLocation": { | |
| 240 "locationType": "LocalPathLocation", | |
| 241 "localPath": "/home/ross/rossgit/tools-iuc/tools/jbrowse2/test-data/bw/merlin.bw" | |
| 242 } | |
| 243 }, | |
| 244 "displays": [ | |
| 245 { | |
| 246 "type": "LinearWiggleDisplay", | |
| 247 "displayId": "merlin.bw-1704349777260-LinearWiggleDisplay" | |
| 248 } | |
| 249 ] | |
| 250 } | |
| 251 ], | |
| 252 "internetAccounts": [ | |
| 253 { | |
| 254 "type": "DropboxOAuthInternetAccount", | |
| 255 "internetAccountId": "dropboxOAuth", | |
| 256 "name": "Dropbox", | |
| 257 "description": "Account to access Dropbox files", | |
| 258 "clientId": "ykjqg1kr23pl1i7" | |
| 259 }, | |
| 260 { | |
| 261 "type": "GoogleDriveOAuthInternetAccount", | |
| 262 "internetAccountId": "googleOAuth", | |
| 263 "name": "Google Drive", | |
| 264 "description": "Account to access Google Drive files", | |
| 265 "clientId": "109518325434-m86s8a5og8ijc5m6n7n8dk7e9586bg9i.apps.googleusercontent.com" | |
| 266 } | |
| 267 ], | |
| 268 "aggregateTextSearchAdapters": [], | |
| 269 "connections": [], | |
| 270 "defaultSession": { | |
| 271 "connectionInstances": [], | |
| 272 "drawerPosition": "right", | |
| 273 "drawerWidth": 384, | |
| 274 "widgets": { | |
| 275 "GridBookmark": { | |
| 276 "id": "GridBookmark", | |
| 277 "type": "GridBookmarkWidget" | |
| 278 }, | |
| 279 "addTrackWidget": { | |
| 280 "id": "addTrackWidget", | |
| 281 "type": "AddTrackWidget", | |
| 282 "view": "oATIzuZAL61OxOyGsWP1l" | |
| 283 }, | |
| 284 "JobsList": { | |
| 285 "id": "JobsList", | |
| 286 "type": "JobsListWidget", | |
| 287 "jobs": [], | |
| 288 "finished": [ | |
| 289 { | |
| 290 "name": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-index", | |
| 291 "statusMessage": "done", | |
| 292 "progressPct": 100 | |
| 293 } | |
| 294 ], | |
| 295 "queued": [], | |
| 296 "aborted": [] | |
| 297 }, | |
| 298 "configEditor": { | |
| 299 "id": "configEditor", | |
| 300 "type": "ConfigurationEditorWidget", | |
| 301 "target": "1838188642fecd9922f419a0e735e755_0.gff3.gz-1704349668492" | |
| 302 }, | |
| 303 "hierarchicalTrackSelector": { | |
| 304 "id": "hierarchicalTrackSelector", | |
| 305 "type": "HierarchicalTrackSelectorWidget", | |
| 306 "initialized": true, | |
| 307 "collapsed": {}, | |
| 308 "view": "oATIzuZAL61OxOyGsWP1l", | |
| 309 "faceted": { | |
| 310 "filterText": "", | |
| 311 "showSparse": false, | |
| 312 "showFilters": true, | |
| 313 "showOptions": false, | |
| 314 "panelWidth": 400 | |
| 315 } | |
| 316 } | |
| 317 }, | |
| 318 "activeWidgets": { | |
| 319 "hierarchicalTrackSelector": "hierarchicalTrackSelector" | |
| 320 }, | |
| 321 "minimized": false, | |
| 322 "id": "0RCNRFfuiied_MUxKv21r", | |
| 323 "name": "New Session 1/4/2024, 5:21:50 PM", | |
| 324 "margin": 0, | |
| 325 "views": [ | |
| 326 { | |
| 327 "id": "oATIzuZAL61OxOyGsWP1l", | |
| 328 "minimized": false, | |
| 329 "type": "LinearGenomeView", | |
| 330 "offsetPx": 0, | |
| 331 "bpPerPx": 113.22935779816514, | |
| 332 "displayedRegions": [ | |
| 333 { | |
| 334 "refName": "Merlin", | |
| 335 "start": 0, | |
| 336 "end": 172788, | |
| 337 "reversed": false, | |
| 338 "assemblyName": "Merlin" | |
| 339 } | |
| 340 ], | |
| 341 "tracks": [ | |
| 342 { | |
| 343 "id": "6q8cZDkFnpribnYm8CCn5", | |
| 344 "type": "FeatureTrack", | |
| 345 "configuration": "3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz-1704349390805", | |
| 346 "minimized": false, | |
| 347 "displays": [ | |
| 348 { | |
| 349 "id": "5lTYaGmlQD_RJMDpG-Mol", | |
| 350 "type": "LinearBasicDisplay", | |
| 351 "configuration": "3eeb95fa8dd6e9d46ac3cd1f3a4b3f4b_0.bed.gz-1704349390805-LinearBasicDisplay" | |
| 352 } | |
| 353 ] | |
| 354 }, | |
| 355 { | |
| 356 "id": "O9bSW2YKphod5uuN1za6E", | |
| 357 "type": "VariantTrack", | |
| 358 "configuration": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277", | |
| 359 "minimized": false, | |
| 360 "displays": [ | |
| 361 { | |
| 362 "id": "31Hdn7-9Dnr0L6PSxiDmf", | |
| 363 "type": "LinearVariantDisplay", | |
| 364 "configuration": "8c3f9b71345db675abafdf2f8e33a6cd_0.vcf.gz-1704349461277-LinearVariantDisplay" | |
| 365 } | |
| 366 ] | |
| 367 }, | |
| 368 { | |
| 369 "id": "IcnRsR2AjMxQq6wiOT9Vi", | |
| 370 "type": "AlignmentsTrack", | |
| 371 "configuration": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556", | |
| 372 "minimized": false, | |
| 373 "displays": [ | |
| 374 { | |
| 375 "id": "Dvu0sQCwrUmkze6Zua8JY", | |
| 376 "type": "LinearAlignmentsDisplay", | |
| 377 "PileupDisplay": { | |
| 378 "id": "ulHQgd0Omh3VttUCKyvPi", | |
| 379 "type": "LinearPileupDisplay", | |
| 380 "heightPreConfig": 205, | |
| 381 "configuration": { | |
| 382 "type": "LinearPileupDisplay", | |
| 383 "displayId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearAlignmentsDisplay_LinearPileupDisplay_xyz" | |
| 384 }, | |
| 385 "filterBy": { | |
| 386 "flagInclude": 0, | |
| 387 "flagExclude": 1540 | |
| 388 }, | |
| 389 "jexlFilters": [], | |
| 390 "showSoftClipping": false | |
| 391 }, | |
| 392 "SNPCoverageDisplay": { | |
| 393 "id": "z_mkwAGHGZCZpvqG0AEMg", | |
| 394 "type": "LinearSNPCoverageDisplay", | |
| 395 "heightPreConfig": 45, | |
| 396 "configuration": { | |
| 397 "type": "LinearSNPCoverageDisplay", | |
| 398 "displayId": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearAlignmentsDisplay_snpcoverage_xyz" | |
| 399 }, | |
| 400 "selectedRendering": "", | |
| 401 "resolution": 1, | |
| 402 "constraints": {}, | |
| 403 "filterBy": { | |
| 404 "flagInclude": 0, | |
| 405 "flagExclude": 1540 | |
| 406 }, | |
| 407 "jexlFilters": [] | |
| 408 }, | |
| 409 "snpCovHeight": 45, | |
| 410 "configuration": "859509e7a79c8f48992e130a2a79b36e_0.bam-1704349533556-LinearAlignmentsDisplay", | |
| 411 "lowerPanelType": "LinearPileupDisplay" | |
| 412 } | |
| 413 ] | |
| 414 }, | |
| 415 { | |
| 416 "id": "sqXxD9i7mkIgJX9bStLFp", | |
| 417 "type": "FeatureTrack", | |
| 418 "configuration": "1838188642fecd9922f419a0e735e755_0.gff3.gz-1704349668492", | |
| 419 "minimized": false, | |
| 420 "displays": [ | |
| 421 { | |
| 422 "id": "ot2hxRedj7L-2eOtTfj47", | |
| 423 "type": "LinearBasicDisplay", | |
| 424 "configuration": "1838188642fecd9922f419a0e735e755_0.gff3.gz-1704349668492-LinearBasicDisplay" | |
| 425 } | |
| 426 ] | |
| 427 }, | |
| 428 { | |
| 429 "id": "w8XYtNAPQ77lYiJ4yfTc_", | |
| 430 "type": "QuantitativeTrack", | |
| 431 "configuration": "merlin.bw-1704349777260", | |
| 432 "minimized": false, | |
| 433 "displays": [ | |
| 434 { | |
| 435 "id": "R7aBFiHHKrly_WAFzxdcN", | |
| 436 "type": "LinearWiggleDisplay", | |
| 437 "configuration": "merlin.bw-1704349777260-LinearWiggleDisplay", | |
| 438 "selectedRendering": "", | |
| 439 "resolution": 1, | |
| 440 "constraints": {} | |
| 441 } | |
| 442 ] | |
| 443 }, | |
| 444 { | |
| 445 "id": "vCT2YxTb4kbBwbjU7y0Nw", | |
| 446 "type": "ReferenceSequenceTrack", | |
| 447 "configuration": "Merlin-1704349310829", | |
| 448 "minimized": false, | |
| 449 "displays": [ | |
| 450 { | |
| 451 "id": "1hj13cpwWU1pHF9KyXyYA", | |
| 452 "type": "LinearReferenceSequenceDisplay", | |
| 453 "heightPreConfig": 50, | |
| 454 "configuration": "Merlin-1704349310829-LinearReferenceSequenceDisplay", | |
| 455 "showForward": true, | |
| 456 "showReverse": true, | |
| 457 "showTranslation": true | |
| 458 } | |
| 459 ] | |
| 460 } | |
| 461 ], | |
| 462 "hideHeader": false, | |
| 463 "hideHeaderOverview": false, | |
| 464 "hideNoTracksActive": false, | |
| 465 "trackSelectorType": "hierarchical", | |
| 466 "showCenterLine": false, | |
| 467 "showCytobandsSetting": true, | |
| 468 "trackLabels": "", | |
| 469 "showGridlines": true, | |
| 470 "showBookmarkHighlights": true, | |
| 471 "showBookmarkLabels": true | |
| 472 } | |
| 473 ], | |
| 474 "sessionAssemblies": [], | |
| 475 "temporaryAssemblies": [], | |
| 476 "focusedViewId": "oATIzuZAL61OxOyGsWP1l" | |
| 477 } | |
| 478 } |
