Mercurial > repos > iuc > jbrowse2
comparison test-data/out/02_remote/config.json @ 0:61add3f58f26 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
| author | iuc |
|---|---|
| date | Thu, 02 Oct 2025 10:19:44 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:61add3f58f26 |
|---|---|
| 1 { | |
| 2 "assemblies": [ | |
| 3 { | |
| 4 "name": "hg19", | |
| 5 "sequence": { | |
| 6 "type": "ReferenceSequenceTrack", | |
| 7 "trackId": "hg19-ReferenceSequenceTrack", | |
| 8 "adapter": { | |
| 9 "type": "BgzipFastaAdapter", | |
| 10 "fastaLocation": { | |
| 11 "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", | |
| 12 "locationType": "UriLocation" | |
| 13 }, | |
| 14 "faiLocation": { | |
| 15 "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai", | |
| 16 "locationType": "UriLocation" | |
| 17 }, | |
| 18 "gziLocation": { | |
| 19 "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi", | |
| 20 "locationType": "UriLocation" | |
| 21 } | |
| 22 } | |
| 23 } | |
| 24 } | |
| 25 ], | |
| 26 "configuration": { | |
| 27 "disableAnalytics": false, | |
| 28 "theme": { | |
| 29 "palette": { | |
| 30 "primary": { | |
| 31 "main": "#0d233f" | |
| 32 }, | |
| 33 "secondary": { | |
| 34 "main": "#721e63" | |
| 35 }, | |
| 36 "tertiary": { | |
| 37 "main": "#135560" | |
| 38 }, | |
| 39 "quaternary": { | |
| 40 "main": "#ffb11d" | |
| 41 } | |
| 42 }, | |
| 43 "typography": { | |
| 44 "fontSize": 10 | |
| 45 } | |
| 46 } | |
| 47 }, | |
| 48 "connections": [], | |
| 49 "defaultSession": { | |
| 50 "name": "hg19", | |
| 51 "views": [ | |
| 52 { | |
| 53 "type": "LinearGenomeView", | |
| 54 "init": { | |
| 55 "assembly": "hg19", | |
| 56 "loc": "1", | |
| 57 "tracks": [ | |
| 58 "f25077b166d61daa5cd442a5341a6778_0_0", | |
| 59 "d356ba515264f7745079b8a8e25265e0_1_0", | |
| 60 "4c55c087663d6bbdba9c10dba1371ef7_2_0", | |
| 61 "0679f3e546fddf3021cce6cc4cdc5683_3_0", | |
| 62 "717916f48c0481fcd916da20c9db8f3d_4_0", | |
| 63 "b7b77cd71a6754bae52b38ac1bfcb1df_5_0", | |
| 64 "d1c14592b12aa3d38a8c9114afb34f7d_6_0", | |
| 65 "b99150c19ec943d2d90eeab328e8ac4e_7_0", | |
| 66 "0e1a5cd1079b0cc284247c45ab58e154_8_0" | |
| 67 ] | |
| 68 } | |
| 69 } | |
| 70 ] | |
| 71 }, | |
| 72 "tracks": [ | |
| 73 { | |
| 74 "type": "QuantitativeTrack", | |
| 75 "trackId": "f25077b166d61daa5cd442a5341a6778_0_0", | |
| 76 "name": "SKBR3 pacbio coverage (NGMLR)", | |
| 77 "adapter": { | |
| 78 "type": "BigWigAdapter", | |
| 79 "bigWigLocation": { | |
| 80 "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw", | |
| 81 "locationType": "UriLocation" | |
| 82 } | |
| 83 }, | |
| 84 "category": [ | |
| 85 "Default" | |
| 86 ], | |
| 87 "assemblyNames": [ | |
| 88 "hg19" | |
| 89 ], | |
| 90 "displays": [ | |
| 91 { | |
| 92 "type": "LinearWiggleDisplay", | |
| 93 "displayId": "f25077b166d61daa5cd442a5341a6778_0_0_LinearWiggleDisplay", | |
| 94 "defaultRendering": "xyplot" | |
| 95 } | |
| 96 ], | |
| 97 "metadata": {} | |
| 98 }, | |
| 99 { | |
| 100 "type": "MultiQuantitativeTrack", | |
| 101 "trackId": "d356ba515264f7745079b8a8e25265e0_1_0", | |
| 102 "name": "SKBR3 pacbio coverage (NGMLR) + 0 other track", | |
| 103 "adapter": { | |
| 104 "type": "MultiWiggleAdapter", | |
| 105 "subadapters": [ | |
| 106 { | |
| 107 "type": "BigWigAdapter", | |
| 108 "name": "SKBR3 pacbio coverage (NGMLR)", | |
| 109 "bigWigLocation": { | |
| 110 "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw", | |
| 111 "locationType": "UriLocation" | |
| 112 } | |
| 113 } | |
| 114 ] | |
| 115 }, | |
| 116 "category": [ | |
| 117 "Default" | |
| 118 ], | |
| 119 "assemblyNames": [ | |
| 120 "hg19" | |
| 121 ], | |
| 122 "displays": [ | |
| 123 { | |
| 124 "type": "MultiLinearWiggleDisplay", | |
| 125 "displayId": "d356ba515264f7745079b8a8e25265e0_1_0_MultiLinearWiggleDisplay", | |
| 126 "defaultRendering": "multirowxy" | |
| 127 } | |
| 128 ], | |
| 129 "metadata": {} | |
| 130 }, | |
| 131 { | |
| 132 "type": "AlignmentsTrack", | |
| 133 "trackId": "4c55c087663d6bbdba9c10dba1371ef7_2_0", | |
| 134 "name": "NA12878 Exome", | |
| 135 "adapter": { | |
| 136 "type": "BamAdapter", | |
| 137 "bamLocation": { | |
| 138 "uri": "https://s3.amazonaws.com/1000genomes/phase3/data/NA12878/exome_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam", | |
| 139 "locationType": "UriLocation" | |
| 140 }, | |
| 141 "index": { | |
| 142 "location": { | |
| 143 "uri": "https://s3.amazonaws.com/1000genomes/phase3/data/NA12878/exome_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam.bai", | |
| 144 "locationType": "UriLocation" | |
| 145 }, | |
| 146 "indexType": "BAI" | |
| 147 }, | |
| 148 "sequenceAdapter": { | |
| 149 "type": "BgzipFastaAdapter", | |
| 150 "fastaLocation": { | |
| 151 "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", | |
| 152 "locationType": "UriLocation" | |
| 153 }, | |
| 154 "faiLocation": { | |
| 155 "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai", | |
| 156 "locationType": "UriLocation" | |
| 157 }, | |
| 158 "gziLocation": { | |
| 159 "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi", | |
| 160 "locationType": "UriLocation" | |
| 161 } | |
| 162 } | |
| 163 }, | |
| 164 "category": [ | |
| 165 "Default" | |
| 166 ], | |
| 167 "assemblyNames": [ | |
| 168 "hg19" | |
| 169 ], | |
| 170 "displays": [ | |
| 171 { | |
| 172 "type": "LinearAlignmentsDisplay", | |
| 173 "displayId": "4c55c087663d6bbdba9c10dba1371ef7_2_0_LinearAlignmentsDisplay" | |
| 174 } | |
| 175 ], | |
| 176 "metadata": {} | |
| 177 }, | |
| 178 { | |
| 179 "type": "AlignmentsTrack", | |
| 180 "trackId": "0679f3e546fddf3021cce6cc4cdc5683_3_0", | |
| 181 "name": "hg_isoforms.fasta_cram", | |
| 182 "adapter": { | |
| 183 "type": "CramAdapter", | |
| 184 "cramLocation": { | |
| 185 "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/alzheimers_isoseq/hq_isoforms.fasta.cram", | |
| 186 "locationType": "UriLocation" | |
| 187 }, | |
| 188 "craiLocation": { | |
| 189 "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/alzheimers_isoseq/hq_isoforms.fasta.cram.crai", | |
| 190 "locationType": "UriLocation" | |
| 191 }, | |
| 192 "sequenceAdapter": { | |
| 193 "type": "BgzipFastaAdapter", | |
| 194 "fastaLocation": { | |
| 195 "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz", | |
| 196 "locationType": "UriLocation" | |
| 197 }, | |
| 198 "faiLocation": { | |
| 199 "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai", | |
| 200 "locationType": "UriLocation" | |
| 201 }, | |
| 202 "gziLocation": { | |
| 203 "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi", | |
| 204 "locationType": "UriLocation" | |
| 205 } | |
| 206 } | |
| 207 }, | |
| 208 "category": [ | |
| 209 "Default" | |
| 210 ], | |
| 211 "assemblyNames": [ | |
| 212 "hg19" | |
| 213 ], | |
| 214 "displays": [ | |
| 215 { | |
| 216 "type": "LinearAlignmentsDisplay", | |
| 217 "displayId": "0679f3e546fddf3021cce6cc4cdc5683_3_0_LinearAlignmentsDisplay" | |
| 218 } | |
| 219 ], | |
| 220 "metadata": {} | |
| 221 }, | |
| 222 { | |
| 223 "type": "HicTrack", | |
| 224 "trackId": "717916f48c0481fcd916da20c9db8f3d_4_0", | |
| 225 "name": "hg_isoforms.fasta_cram", | |
| 226 "adapter": { | |
| 227 "type": "HicAdapter", | |
| 228 "hicLocation": { | |
| 229 "uri": "https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic", | |
| 230 "locationType": "UriLocation" | |
| 231 } | |
| 232 }, | |
| 233 "category": [ | |
| 234 "Default" | |
| 235 ], | |
| 236 "assemblyNames": [ | |
| 237 "hg19" | |
| 238 ], | |
| 239 "displays": [ | |
| 240 { | |
| 241 "type": "LinearHicDisplay", | |
| 242 "displayId": "717916f48c0481fcd916da20c9db8f3d_4_0_LinearHicDisplay" | |
| 243 } | |
| 244 ], | |
| 245 "metadata": {} | |
| 246 }, | |
| 247 { | |
| 248 "type": "VariantTrack", | |
| 249 "trackId": "b7b77cd71a6754bae52b38ac1bfcb1df_5_0", | |
| 250 "name": "HG002 dbVar variant calls", | |
| 251 "adapter": { | |
| 252 "type": "VcfTabixAdapter", | |
| 253 "vcfGzLocation": { | |
| 254 "uri": "https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/vcf/nstd175.GRCh37.variant_call.vcf.gz", | |
| 255 "locationType": "UriLocation" | |
| 256 }, | |
| 257 "index": { | |
| 258 "location": { | |
| 259 "uri": "https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/vcf/nstd175.GRCh37.variant_call.vcf.gz.tbi", | |
| 260 "locationType": "UriLocation" | |
| 261 }, | |
| 262 "indexType": "TBI" | |
| 263 } | |
| 264 }, | |
| 265 "category": [ | |
| 266 "Default" | |
| 267 ], | |
| 268 "assemblyNames": [ | |
| 269 "hg19" | |
| 270 ], | |
| 271 "displays": [ | |
| 272 { | |
| 273 "type": "LinearVariantDisplay", | |
| 274 "displayId": "b7b77cd71a6754bae52b38ac1bfcb1df_5_0_LinearVariantDisplay" | |
| 275 } | |
| 276 ], | |
| 277 "formatDetails": {}, | |
| 278 "metadata": {} | |
| 279 }, | |
| 280 { | |
| 281 "type": "VariantTrack", | |
| 282 "trackId": "d1c14592b12aa3d38a8c9114afb34f7d_6_0", | |
| 283 "name": "truthset_somaticSVs_COLO829", | |
| 284 "adapter": { | |
| 285 "type": "VcfAdapter", | |
| 286 "vcfLocation": { | |
| 287 "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/COLO829/truthset_somaticSVs_COLO829.vcf", | |
| 288 "locationType": "UriLocation" | |
| 289 } | |
| 290 }, | |
| 291 "category": [ | |
| 292 "Default" | |
| 293 ], | |
| 294 "assemblyNames": [ | |
| 295 "hg19" | |
| 296 ], | |
| 297 "displays": [ | |
| 298 { | |
| 299 "type": "LinearVariantDisplay", | |
| 300 "displayId": "d1c14592b12aa3d38a8c9114afb34f7d_6_0_LinearVariantDisplay" | |
| 301 } | |
| 302 ], | |
| 303 "formatDetails": {}, | |
| 304 "metadata": {} | |
| 305 }, | |
| 306 { | |
| 307 "type": "FeatureTrack", | |
| 308 "trackId": "b99150c19ec943d2d90eeab328e8ac4e_7_0", | |
| 309 "name": "Gencode v36 (GRCh37 liftover)", | |
| 310 "adapter": { | |
| 311 "type": "Gff3TabixAdapter", | |
| 312 "gffGzLocation": { | |
| 313 "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gencode/gencode.v36lift37.annotation.sort.gff3.gz", | |
| 314 "locationType": "UriLocation" | |
| 315 }, | |
| 316 "index": { | |
| 317 "location": { | |
| 318 "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gencode/gencode.v36lift37.annotation.sort.gff3.gz.tbi", | |
| 319 "locationType": "UriLocation" | |
| 320 }, | |
| 321 "indexType": "TBI" | |
| 322 } | |
| 323 }, | |
| 324 "category": [ | |
| 325 "Default" | |
| 326 ], | |
| 327 "assemblyNames": [ | |
| 328 "hg19" | |
| 329 ], | |
| 330 "displays": [ | |
| 331 { | |
| 332 "type": "LinearBasicDisplay", | |
| 333 "displayId": "b99150c19ec943d2d90eeab328e8ac4e_7_0_LinearBasicDisplay", | |
| 334 "renderer": { | |
| 335 "type": "SvgFeatureRenderer", | |
| 336 "showLabels": true, | |
| 337 "showDescriptions": true, | |
| 338 "labels": { | |
| 339 "name": "jexl:get(feature,'name') || get(feature,'id')", | |
| 340 "description": "jexl:get(feature,'note') || get(feature,'description')" | |
| 341 }, | |
| 342 "displayMode": "normal", | |
| 343 "maxHeight": 600 | |
| 344 } | |
| 345 } | |
| 346 ], | |
| 347 "formatDetails": { | |
| 348 "depth": 1 | |
| 349 }, | |
| 350 "metadata": {} | |
| 351 }, | |
| 352 { | |
| 353 "type": "FeatureTrack", | |
| 354 "trackId": "0e1a5cd1079b0cc284247c45ab58e154_8_0", | |
| 355 "name": "wgEncodeDukeMapabilityRegionsExcludable", | |
| 356 "adapter": { | |
| 357 "type": "BedTabixAdapter", | |
| 358 "bedGzLocation": { | |
| 359 "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/mappability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz", | |
| 360 "locationType": "UriLocation" | |
| 361 }, | |
| 362 "index": { | |
| 363 "location": { | |
| 364 "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/mappability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz.tbi", | |
| 365 "locationType": "UriLocation" | |
| 366 }, | |
| 367 "indexType": "TBI" | |
| 368 } | |
| 369 }, | |
| 370 "category": [ | |
| 371 "Default" | |
| 372 ], | |
| 373 "assemblyNames": [ | |
| 374 "hg19" | |
| 375 ], | |
| 376 "displays": [ | |
| 377 { | |
| 378 "type": "LinearBasicDisplay", | |
| 379 "displayId": "0e1a5cd1079b0cc284247c45ab58e154_8_0_LinearBasicDisplay", | |
| 380 "renderer": { | |
| 381 "type": "SvgFeatureRenderer", | |
| 382 "showLabels": true, | |
| 383 "showDescriptions": true, | |
| 384 "labels": { | |
| 385 "name": "jexl:get(feature,'name') || get(feature,'id')", | |
| 386 "description": "jexl:get(feature,'note') || get(feature,'description')" | |
| 387 }, | |
| 388 "displayMode": "normal", | |
| 389 "maxHeight": 600 | |
| 390 } | |
| 391 } | |
| 392 ], | |
| 393 "formatDetails": { | |
| 394 "depth": 1 | |
| 395 }, | |
| 396 "metadata": {} | |
| 397 } | |
| 398 ], | |
| 399 "plugins": [] | |
| 400 } |
