@jbrowse/cli 1.5.1 → 1.5.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (6) hide show
  1. package/README.md +10 -10
  2. package/lib/commands/add-assembly.js +5 -5
  3. package/lib/commands/add-track.d.ts +79 -7
  4. package/lib/commands/add-track.js +45 -66
  5. package/oclif.manifest.json +1 -1
  6. package/package.json +4 -3
package/README.md CHANGED
@@ -4,7 +4,7 @@ id: cli
4
4
  toplevel: true
5
5
  ---
6
6
 
7
- This document covers the CLI tools.
7
+ This document covers the CLI tools. Note: for @jbrowse/img static export tool, see https://www.npmjs.com/package/@jbrowse/img
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8
 
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9
  ## Installation
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10
 
@@ -157,7 +157,7 @@ EXAMPLES
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  $ jbrowse add-assembly myfile.fa.gz --load copy
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  ```
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160
- _See code: [src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.1/products/jbrowse-cli/src/commands/add-assembly.ts)_
160
+ _See code: [src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/add-assembly.ts)_
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161
 
162
162
  ## `jbrowse add-connection CONNECTIONURLORPATH`
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@@ -211,7 +211,7 @@ EXAMPLES
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  /path/to/jb2/installation/config.json
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  ```
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213
 
214
- _See code: [src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.1/products/jbrowse-cli/src/commands/add-connection.ts)_
214
+ _See code: [src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/add-connection.ts)_
215
215
 
216
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  ## `jbrowse add-track TRACK`
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217
 
@@ -285,7 +285,7 @@ EXAMPLES
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  $ jbrowse add-track /url/relative/path.bam --load inPlace
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  ```
287
287
 
288
- _See code: [src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.1/products/jbrowse-cli/src/commands/add-track.ts)_
288
+ _See code: [src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/add-track.ts)_
289
289
 
290
290
  ## `jbrowse add-track-json TRACK`
291
291
 
@@ -310,7 +310,7 @@ EXAMPLES
310
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  $ jbrowse add-track-json track.json --update
311
311
  ```
312
312
 
313
- _See code: [src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.1/products/jbrowse-cli/src/commands/add-track-json.ts)_
313
+ _See code: [src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/add-track-json.ts)_
314
314
 
315
315
  ## `jbrowse admin-server`
316
316
 
@@ -336,7 +336,7 @@ EXAMPLES
336
336
  $ jbrowse admin-server -p 8888
337
337
  ```
338
338
 
339
- _See code: [src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.1/products/jbrowse-cli/src/commands/admin-server.ts)_
339
+ _See code: [src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/admin-server.ts)_
340
340
 
341
341
  ## `jbrowse create LOCALPATH`
342
342
 
@@ -380,7 +380,7 @@ EXAMPLES
380
380
  $ jbrowse create --listVersions
381
381
  ```
382
382
 
383
- _See code: [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.1/products/jbrowse-cli/src/commands/create.ts)_
383
+ _See code: [src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/create.ts)_
384
384
 
385
385
  ## `jbrowse help [COMMAND]`
386
386
 
@@ -434,7 +434,7 @@ EXAMPLES
434
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  $ jbrowse set-default-session --currentSession # Prints out current default session
435
435
  ```
436
436
 
437
- _See code: [src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.1/products/jbrowse-cli/src/commands/set-default-session.ts)_
437
+ _See code: [src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/set-default-session.ts)_
438
438
 
439
439
  ## `jbrowse text-index`
440
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@@ -490,7 +490,7 @@ EXAMPLES
490
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  $ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes
491
491
  ```
492
492
 
493
- _See code: [src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.1/products/jbrowse-cli/src/commands/text-index.ts)_
493
+ _See code: [src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/text-index.ts)_
494
494
 
495
495
  ## `jbrowse upgrade [LOCALPATH]`
496
496
 
@@ -536,7 +536,7 @@ EXAMPLES
536
536
  $ jbrowse upgrade --nightly
537
537
  ```
538
538
 
539
- _See code: [src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.1/products/jbrowse-cli/src/commands/upgrade.ts)_
539
+ _See code: [src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v1.5.2/products/jbrowse-cli/src/commands/upgrade.ts)_
540
540
 
541
541
  <!-- commandsstop -->
542
542
 
package/lib/commands/add-assembly.js CHANGED
@@ -5,7 +5,7 @@ const command_1 = require("@oclif/command");
5
5
  const fs_1 = (0, tslib_1.__importDefault)(require("fs"));
6
6
  const path_1 = (0, tslib_1.__importDefault)(require("path"));
7
7
  const base_1 = (0, tslib_1.__importDefault)(require("../base"));
8
- const fsPromises = fs_1.default.promises;
8
+ const { rename, copyFile, mkdir, symlink } = fs_1.default.promises;
9
9
  function isValidJSON(string) {
10
10
  try {
11
11
  JSON.parse(string);
@@ -206,7 +206,7 @@ class AddAssembly extends base_1.default {
206
206
  const { args: runArgs, flags: runFlags } = this.parse(AddAssembly);
207
207
  const output = runFlags.target || runFlags.out || '.';
208
208
  if (!(await exists(output))) {
209
- await fsPromises.mkdir(output, { recursive: true });
209
+ await mkdir(output, { recursive: true });
210
210
  }
211
211
  const isDir = fs_1.default.statSync(output).isDirectory();
212
212
  this.target = isDir ? `${output}/config.json` : output;
@@ -347,7 +347,7 @@ class AddAssembly extends base_1.default {
347
347
  if (!filePath) {
348
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  return undefined;
349
349
  }
350
- return fsPromises.copyFile(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
350
+ return copyFile(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
351
351
  }));
352
352
  return true;
353
353
  }
@@ -356,7 +356,7 @@ class AddAssembly extends base_1.default {
356
356
  if (!filePath) {
357
357
  return undefined;
358
358
  }
359
- return fsPromises.symlink(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
359
+ return symlink(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
360
360
  }));
361
361
  return true;
362
362
  }
@@ -365,7 +365,7 @@ class AddAssembly extends base_1.default {
365
365
  if (!filePath) {
366
366
  return undefined;
367
367
  }
368
- return fsPromises.rename(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
368
+ return rename(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
369
369
  }));
370
370
  return true;
371
371
  }
package/lib/commands/add-track.d.ts CHANGED
@@ -42,21 +42,17 @@ export default class AddTrack extends JBrowseCommand {
42
42
  index: string;
43
43
  index2?: undefined;
44
44
  } | {
45
- file?: undefined;
45
+ file: string;
46
46
  index?: undefined;
47
47
  index2?: undefined;
48
48
  } | {
49
- file: string;
50
- index: undefined;
49
+ file?: undefined;
50
+ index?: undefined;
51
51
  index2?: undefined;
52
52
  } | {
53
53
  file: string;
54
54
  index: string;
55
55
  index2: string;
56
- } | {
57
- file: string;
58
- index?: undefined;
59
- index2?: undefined;
60
56
  };
61
57
  guessAdapter(fileName: string, protocol: string, index?: string): {
62
58
  type: string;
@@ -67,7 +63,9 @@ export default class AddTrack extends JBrowseCommand {
67
63
  };
68
64
  cramLocation?: undefined;
69
65
  craiLocation?: undefined;
66
+ gffLocation?: undefined;
70
67
  gffGzLocation?: undefined;
68
+ gtfLocation?: undefined;
71
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  vcfLocation?: undefined;
72
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  vcfGzLocation?: undefined;
73
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  bedGzLocation?: undefined;
@@ -87,7 +85,9 @@ export default class AddTrack extends JBrowseCommand {
87
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  craiLocation: UriLocation | LocalPathLocation;
88
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  bamLocation?: undefined;
89
87
  index?: undefined;
88
+ gffLocation?: undefined;
90
89
  gffGzLocation?: undefined;
90
+ gtfLocation?: undefined;
91
91
  vcfLocation?: undefined;
92
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  vcfGzLocation?: undefined;
93
93
  bedGzLocation?: undefined;
@@ -103,11 +103,13 @@ export default class AddTrack extends JBrowseCommand {
103
103
  pafLocation?: undefined;
104
104
  } | {
105
105
  type: string;
106
+ gffLocation: UriLocation | LocalPathLocation;
106
107
  bamLocation?: undefined;
107
108
  index?: undefined;
108
109
  cramLocation?: undefined;
109
110
  craiLocation?: undefined;
110
111
  gffGzLocation?: undefined;
112
+ gtfLocation?: undefined;
111
113
  vcfLocation?: undefined;
112
114
  vcfGzLocation?: undefined;
113
115
  bedGzLocation?: undefined;
@@ -131,6 +133,30 @@ export default class AddTrack extends JBrowseCommand {
131
133
  bamLocation?: undefined;
132
134
  cramLocation?: undefined;
133
135
  craiLocation?: undefined;
136
+ gffLocation?: undefined;
137
+ gtfLocation?: undefined;
138
+ vcfLocation?: undefined;
139
+ vcfGzLocation?: undefined;
140
+ bedGzLocation?: undefined;
141
+ bigBedLocation?: undefined;
142
+ bigWigLocation?: undefined;
143
+ fastaLocation?: undefined;
144
+ faiLocation?: undefined;
145
+ gziLocation?: undefined;
146
+ twoBitLocation?: undefined;
147
+ rootUrlTemplate?: undefined;
148
+ endpoint?: undefined;
149
+ hicLocation?: undefined;
150
+ pafLocation?: undefined;
151
+ } | {
152
+ type: string;
153
+ gtfLocation: UriLocation | LocalPathLocation;
154
+ bamLocation?: undefined;
155
+ index?: undefined;
156
+ cramLocation?: undefined;
157
+ craiLocation?: undefined;
158
+ gffLocation?: undefined;
159
+ gffGzLocation?: undefined;
134
160
  vcfLocation?: undefined;
135
161
  vcfGzLocation?: undefined;
136
162
  bedGzLocation?: undefined;
@@ -151,7 +177,9 @@ export default class AddTrack extends JBrowseCommand {
151
177
  index?: undefined;
152
178
  cramLocation?: undefined;
153
179
  craiLocation?: undefined;
180
+ gffLocation?: undefined;
154
181
  gffGzLocation?: undefined;
182
+ gtfLocation?: undefined;
155
183
  vcfGzLocation?: undefined;
156
184
  bedGzLocation?: undefined;
157
185
  bigBedLocation?: undefined;
@@ -174,8 +202,32 @@ export default class AddTrack extends JBrowseCommand {
174
202
  bamLocation?: undefined;
175
203
  cramLocation?: undefined;
176
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  craiLocation?: undefined;
205
+ gffLocation?: undefined;
206
+ gffGzLocation?: undefined;
207
+ gtfLocation?: undefined;
208
+ vcfLocation?: undefined;
209
+ bedGzLocation?: undefined;
210
+ bigBedLocation?: undefined;
211
+ bigWigLocation?: undefined;
212
+ fastaLocation?: undefined;
213
+ faiLocation?: undefined;
214
+ gziLocation?: undefined;
215
+ twoBitLocation?: undefined;
216
+ rootUrlTemplate?: undefined;
217
+ endpoint?: undefined;
218
+ hicLocation?: undefined;
219
+ pafLocation?: undefined;
220
+ } | {
221
+ type: string;
222
+ bamLocation?: undefined;
223
+ index?: undefined;
224
+ cramLocation?: undefined;
225
+ craiLocation?: undefined;
226
+ gffLocation?: undefined;
177
227
  gffGzLocation?: undefined;
228
+ gtfLocation?: undefined;
178
229
  vcfLocation?: undefined;
230
+ vcfGzLocation?: undefined;
179
231
  bedGzLocation?: undefined;
180
232
  bigBedLocation?: undefined;
181
233
  bigWigLocation?: undefined;
@@ -197,7 +249,9 @@ export default class AddTrack extends JBrowseCommand {
197
249
  bamLocation?: undefined;
198
250
  cramLocation?: undefined;
199
251
  craiLocation?: undefined;
252
+ gffLocation?: undefined;
200
253
  gffGzLocation?: undefined;
254
+ gtfLocation?: undefined;
201
255
  vcfLocation?: undefined;
202
256
  vcfGzLocation?: undefined;
203
257
  bigBedLocation?: undefined;
@@ -217,7 +271,9 @@ export default class AddTrack extends JBrowseCommand {
217
271
  index?: undefined;
218
272
  cramLocation?: undefined;
219
273
  craiLocation?: undefined;
274
+ gffLocation?: undefined;
220
275
  gffGzLocation?: undefined;
276
+ gtfLocation?: undefined;
221
277
  vcfLocation?: undefined;
222
278
  vcfGzLocation?: undefined;
223
279
  bedGzLocation?: undefined;
@@ -237,7 +293,9 @@ export default class AddTrack extends JBrowseCommand {
237
293
  index?: undefined;
238
294
  cramLocation?: undefined;
239
295
  craiLocation?: undefined;
296
+ gffLocation?: undefined;
240
297
  gffGzLocation?: undefined;
298
+ gtfLocation?: undefined;
241
299
  vcfLocation?: undefined;
242
300
  vcfGzLocation?: undefined;
243
301
  bedGzLocation?: undefined;
@@ -258,7 +316,9 @@ export default class AddTrack extends JBrowseCommand {
258
316
  index?: undefined;
259
317
  cramLocation?: undefined;
260
318
  craiLocation?: undefined;
319
+ gffLocation?: undefined;
261
320
  gffGzLocation?: undefined;
321
+ gtfLocation?: undefined;
262
322
  vcfLocation?: undefined;
263
323
  vcfGzLocation?: undefined;
264
324
  bedGzLocation?: undefined;
@@ -279,7 +339,9 @@ export default class AddTrack extends JBrowseCommand {
279
339
  index?: undefined;
280
340
  cramLocation?: undefined;
281
341
  craiLocation?: undefined;
342
+ gffLocation?: undefined;
282
343
  gffGzLocation?: undefined;
344
+ gtfLocation?: undefined;
283
345
  vcfLocation?: undefined;
284
346
  vcfGzLocation?: undefined;
285
347
  bedGzLocation?: undefined;
@@ -297,7 +359,9 @@ export default class AddTrack extends JBrowseCommand {
297
359
  index?: undefined;
298
360
  cramLocation?: undefined;
299
361
  craiLocation?: undefined;
362
+ gffLocation?: undefined;
300
363
  gffGzLocation?: undefined;
364
+ gtfLocation?: undefined;
301
365
  vcfLocation?: undefined;
302
366
  vcfGzLocation?: undefined;
303
367
  bedGzLocation?: undefined;
@@ -317,7 +381,9 @@ export default class AddTrack extends JBrowseCommand {
317
381
  index?: undefined;
318
382
  cramLocation?: undefined;
319
383
  craiLocation?: undefined;
384
+ gffLocation?: undefined;
320
385
  gffGzLocation?: undefined;
386
+ gtfLocation?: undefined;
321
387
  vcfLocation?: undefined;
322
388
  vcfGzLocation?: undefined;
323
389
  bedGzLocation?: undefined;
@@ -337,7 +403,9 @@ export default class AddTrack extends JBrowseCommand {
337
403
  index?: undefined;
338
404
  cramLocation?: undefined;
339
405
  craiLocation?: undefined;
406
+ gffLocation?: undefined;
340
407
  gffGzLocation?: undefined;
408
+ gtfLocation?: undefined;
341
409
  vcfLocation?: undefined;
342
410
  vcfGzLocation?: undefined;
343
411
  bedGzLocation?: undefined;
@@ -357,7 +425,9 @@ export default class AddTrack extends JBrowseCommand {
357
425
  index?: undefined;
358
426
  cramLocation?: undefined;
359
427
  craiLocation?: undefined;
428
+ gffLocation?: undefined;
360
429
  gffGzLocation?: undefined;
430
+ gtfLocation?: undefined;
361
431
  vcfLocation?: undefined;
362
432
  vcfGzLocation?: undefined;
363
433
  bedGzLocation?: undefined;
@@ -377,7 +447,9 @@ export default class AddTrack extends JBrowseCommand {
377
447
  index?: undefined;
378
448
  cramLocation?: undefined;
379
449
  craiLocation?: undefined;
450
+ gffLocation?: undefined;
380
451
  gffGzLocation?: undefined;
452
+ gtfLocation?: undefined;
381
453
  vcfLocation?: undefined;
382
454
  vcfGzLocation?: undefined;
383
455
  bedGzLocation?: undefined;
package/lib/commands/add-track.js CHANGED
@@ -6,14 +6,16 @@ const fs_1 = (0, tslib_1.__importDefault)(require("fs"));
6
6
  const path_1 = (0, tslib_1.__importDefault)(require("path"));
7
7
  const json_parse_better_errors_1 = (0, tslib_1.__importDefault)(require("json-parse-better-errors"));
8
8
  const base_1 = (0, tslib_1.__importDefault)(require("../base"));
9
- const fsPromises = fs_1.default.promises;
9
+ const { copyFile, rename, symlink, lstat, unlink } = fs_1.default.promises;
10
+ const { COPYFILE_EXCL } = fs_1.default.constants;
11
+ const isUrl = (loc) => loc === null || loc === void 0 ? void 0 : loc.match(/^https?:\/\//);
10
12
  class AddTrack extends base_1.default {
11
13
  async run() {
12
14
  const { args: runArgs, flags: runFlags } = this.parse(AddTrack);
13
15
  const { track: argsTrack } = runArgs;
14
16
  const { config, skipCheck, force, overwrite, category, description, load, subDir, target, protocol, out, indexFile: index, } = runFlags;
15
17
  const output = target || out || '.';
16
- const isDir = (await fsPromises.lstat(output)).isDirectory();
18
+ const isDir = (await lstat(output)).isDirectory();
17
19
  this.target = isDir ? `${output}/config.json` : output;
18
20
  let { trackType, trackId, name, assemblyNames } = runFlags;
19
21
  const configDirectory = path_1.default.dirname(this.target);
@@ -27,7 +29,6 @@ class AddTrack extends base_1.default {
27
29
  }
28
30
  }
29
31
  const location = argsTrack;
30
- const isUrl = (loc) => loc === null || loc === void 0 ? void 0 : loc.match(/^https?:\/\//);
31
32
  const inPlace = load === 'inPlace';
32
33
  const useIndex = isUrl(index) || inPlace || index;
33
34
  const effectiveLocation = isUrl(location) || inPlace
@@ -78,11 +79,9 @@ class AddTrack extends base_1.default {
78
79
  this.debug(`Assembly name(s) is :${assemblyNames}`);
79
80
  const configObj = config ? (0, json_parse_better_errors_1.default)(config) : {};
80
81
  const trackConfig = Object.assign({ type: trackType, trackId,
81
- name, category: category ? category.split(',').map(c => c.trim()) : undefined, assemblyNames: assemblyNames.split(',').map(a => a.trim()), adapter }, configObj);
82
+ name,
83
+ adapter, category: category === null || category === void 0 ? void 0 : category.split(',').map(c => c.trim()), assemblyNames: assemblyNames.split(',').map(a => a.trim()), description }, configObj);
82
84
  this.debug(`Track location: ${location}, index: ${adapter ? adapter.index : ''}`);
83
- if (description) {
84
- trackConfig.description = description;
85
- }
86
85
  // any special track modifications go here
87
86
  switch (trackType) {
88
87
  case 'AlignmentsTrack': {
@@ -113,56 +112,27 @@ class AddTrack extends base_1.default {
113
112
  else {
114
113
  configContents.tracks.push(trackConfig);
115
114
  }
116
- // copy/symlinks/moves the track into the jbrowse installation directory
117
- const filePaths = Object.values(this.guessFileNames(location, index)).filter(f => !!f);
118
- const destinationFn = (dir, file) => path_1.default.join(dir, subDir, path_1.default.basename(file));
119
- switch (load) {
120
- case 'copy': {
121
- await Promise.all(filePaths.map(async (filePath) => {
122
- const dest = destinationFn(configDirectory, filePath);
123
- try {
124
- if (force && fs_1.default.existsSync(dest)) {
125
- await fsPromises.unlink(dest);
126
- }
127
- }
128
- catch (e) {
129
- this.error(e instanceof Error ? e : `${e}`);
130
- }
131
- return fsPromises.copyFile(filePath, dest, fs_1.default.constants.COPYFILE_EXCL);
132
- }));
133
- break;
134
- }
135
- case 'symlink': {
136
- await Promise.all(filePaths.map(async (filePath) => {
137
- const dest = destinationFn(configDirectory, filePath);
138
- try {
139
- if (force && fs_1.default.existsSync(dest)) {
140
- await fsPromises.unlink(dest);
141
- }
142
- }
143
- catch (e) {
144
- this.error(e instanceof Error ? e : `${e}`);
145
- }
146
- return fsPromises.symlink(filePath, dest);
147
- }));
148
- break;
115
+ const filePaths = Object.values(this.guessFileNames(location, index)).filter((f) => !!f);
116
+ // get path of destination, and remove file at that path if it exists and
117
+ // force is set
118
+ const destinationFn = async (dir, file) => {
119
+ const dest = path_1.default.join(dir, subDir, path_1.default.basename(file));
120
+ if (force && fs_1.default.existsSync(dest)) {
121
+ await unlink(dest);
149
122
  }
150
- case 'move': {
151
- await Promise.all(filePaths.map(async (filePath) => {
152
- const dest = destinationFn(configDirectory, filePath);
153
- try {
154
- if (force && fs_1.default.existsSync(dest)) {
155
- await fsPromises.unlink(dest);
156
- }
157
- }
158
- catch (e) {
159
- this.error(e instanceof Error ? e : `${e}`);
160
- }
161
- return fsPromises.rename(filePath, dest);
162
- }));
163
- break;
123
+ return dest;
124
+ };
125
+ const callbacks = {
126
+ copy: (src, dest) => copyFile(src, dest, COPYFILE_EXCL),
127
+ move: (src, dest) => rename(src, dest),
128
+ symlink: (src, dest) => symlink(src, dest),
129
+ };
130
+ await Promise.all(filePaths.map(async (src) => {
131
+ const dest = await destinationFn(configDirectory, src);
132
+ if (load === 'copy' || load === 'move' || load === 'symlink') {
133
+ return callbacks[load](src, dest);
164
134
  }
165
- }
135
+ }));
166
136
  this.debug(`Writing configuration to file ${this.target}`);
167
137
  await this.writeJsonFile(this.target, configContents);
168
138
  this.log(`${idx !== -1 ? 'Overwrote' : 'Added'} track "${name}" ${idx !== -1 ? 'in' : 'to'} ${this.target}`);
@@ -177,28 +147,34 @@ class AddTrack extends base_1.default {
177
147
  if (/\.cram$/i.test(fileName)) {
178
148
  return {
179
149
  file: fileName,
180
- index: `${fileName}.crai`,
150
+ index: index || `${fileName}.crai`,
181
151
  };
182
152
  }
183
153
  if (/\.gff3?$/i.test(fileName)) {
184
- return {};
154
+ return {
155
+ file: fileName,
156
+ };
185
157
  }
186
158
  if (/\.gff3?\.b?gz$/i.test(fileName)) {
187
159
  return {
188
160
  file: fileName,
189
- index: `${fileName}.tbi`,
161
+ index: index || `${fileName}.tbi`,
190
162
  };
191
163
  }
192
164
  if (/\.gtf?$/i.test(fileName)) {
193
- return {};
165
+ return {
166
+ file: fileName,
167
+ };
194
168
  }
195
169
  if (/\.vcf$/i.test(fileName)) {
196
- return {};
170
+ return {
171
+ file: fileName,
172
+ };
197
173
  }
198
174
  if (/\.vcf\.b?gz$/i.test(fileName)) {
199
175
  return {
200
176
  file: fileName,
201
- index: `${fileName}.tbi`,
177
+ index: index || `${fileName}.tbi`,
202
178
  };
203
179
  }
204
180
  if (/\.vcf\.idx$/i.test(fileName)) {
@@ -219,13 +195,11 @@ class AddTrack extends base_1.default {
219
195
  if (/\.(bb|bigbed)$/i.test(fileName)) {
220
196
  return {
221
197
  file: fileName,
222
- index: undefined,
223
198
  };
224
199
  }
225
200
  if (/\.(bw|bigwig)$/i.test(fileName)) {
226
201
  return {
227
202
  file: fileName,
228
- index: undefined,
229
203
  };
230
204
  }
231
205
  if (/\.(fa|fasta|fas|fna|mfa)$/i.test(fileName)) {
@@ -278,7 +252,10 @@ class AddTrack extends base_1.default {
278
252
  return { uri: location, locationType: 'UriLocation' };
279
253
  }
280
254
  if (protocol === 'localPath') {
281
- return { localPath: location, locationType: 'LocalPathLocation' };
255
+ return {
256
+ localPath: location,
257
+ locationType: 'LocalPathLocation',
258
+ };
282
259
  }
283
260
  throw new Error(`invalid protocol ${protocol}`);
284
261
  }
@@ -301,7 +278,8 @@ class AddTrack extends base_1.default {
301
278
  }
302
279
  if (/\.gff3?$/i.test(fileName)) {
303
280
  return {
304
- type: 'UNSUPPORTED',
281
+ type: 'Gff3Adapter',
282
+ gffLocation: makeLocation(fileName),
305
283
  };
306
284
  }
307
285
  if (/\.gff3?\.b?gz$/i.test(fileName)) {
@@ -316,7 +294,8 @@ class AddTrack extends base_1.default {
316
294
  }
317
295
  if (/\.gtf?$/i.test(fileName)) {
318
296
  return {
319
- type: 'UNSUPPORTED',
297
+ type: 'GtfAdapter',
298
+ gtfLocation: makeLocation(fileName),
320
299
  };
321
300
  }
322
301
  if (/\.vcf$/i.test(fileName)) {
package/oclif.manifest.json CHANGED
@@ -1 +1 @@
1
- {"version":"1.5.1","commands":{"add-assembly":{"id":"add-assembly","description":"Add an assembly to a JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory","$ jbrowse add-assembly GRCh38.fa --load copy","","# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2","$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy","","# force indexedFasta for add-assembly without relying on file extension","$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy","","# add displayName for an assembly","$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName \"Homo sapiens (hg38)\"","","# use chrom.sizes file for assembly instead of a fasta file","$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace","","# add assembly from preconfigured json file, expert option","$ jbrowse add-assembly GRCh38.config.json --load copy","","# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed","$ jbrowse add-assembly https://example.com/data/sample.2bit","","# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists","$ jbrowse add-assembly myfile.fa.gz --load copy"],"flags":{"type":{"name":"type","type":"option","char":"t","description":"type of sequence, by default inferred from sequence file\n\nindexedFasta An index FASTA (e.g. .fa or .fasta) file;\n can optionally specify --faiLocation\n\nbgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file;\n can optionally specify --faiLocation and/or --gziLocation\n\ntwoBit A twoBit (e.g. .2bit) file\n\nchromSizes A chromosome sizes (e.g. .chrom.sizes) file\n\ncustom Either a JSON file location or inline JSON that defines a custom\n sequence adapter; must provide --name if using inline JSON","options":["indexedFasta","bgzipFasta","twoBit","chromSizes","custom"]},"name":{"name":"name","type":"option","char":"n","description":"Name of the assembly; if not specified, will be guessed using the sequence file name"},"alias":{"name":"alias","type":"option","char":"a","description":"An alias for the assembly name (e.g. \"hg38\" if the name of the assembly is \"GRCh38\");\ncan be specified multiple times"},"displayName":{"name":"displayName","type":"option","description":"The display name to specify for the assembly, e.g. \"Homo sapiens (hg38)\" while the name can be a shorter identifier like \"hg38\""},"faiLocation":{"name":"faiLocation","type":"option","description":"[default: <fastaLocation>.fai] FASTA index file or URL"},"gziLocation":{"name":"gziLocation","type":"option","description":"[default: <fastaLocation>.gzi] FASTA gzip index file or URL"},"refNameAliases":{"name":"refNameAliases","type":"option","description":"Reference sequence name aliases file or URL; assumed to be a tab-separated aliases\nfile unless --refNameAliasesType is specified"},"refNameAliasesType":{"name":"refNameAliasesType","type":"option","description":"Type of aliases defined by --refNameAliases; if \"custom\", --refNameAliases is either\na JSON file location or inline JSON that defines a custom sequence adapter","options":["aliases","custom"]},"refNameColors":{"name":"refNameColors","type":"option","description":"A comma-separated list of color strings for the reference sequence names; will cycle\nthrough colors if there are fewer colors than sequences"},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent"},"out":{"name":"out","type":"option","description":"synonym for target"},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"load":{"name":"load","type":"option","char":"l","description":"Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations","options":["copy","symlink","move","inPlace"]},"skipCheck":{"name":"skipCheck","type":"boolean","description":"Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory","allowNo":false},"overwrite":{"name":"overwrite","type":"boolean","description":"Overwrite existing assembly if one with the same name exists","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Equivalent to `--skipCheck --overwrite`","allowNo":false}},"args":[{"name":"sequence","description":"sequence file or URL\n\nIf TYPE is indexedFasta or bgzipFasta, the index file defaults to <location>.fai\nand can be optionally specified with --faiLocation\nIf TYPE is bgzipFasta, the gzip index file defaults to <location>.gzi and can be\noptionally specified with --gziLocation","required":true}]},"add-connection":{"id":"add-connection","description":"Add a connection to a JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse add-connection http://mysite.com/jbrowse/data/","$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection","$ jbrowse add-connection http://mysite.com/path/to/hub.txt --assemblyName hg19","$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection --assemblyName hg19","$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{\"uri\":{\"url\":\"https://mysite.com/path/to/custom\"}, \"locationType\": \"UriLocation\"}' --assemblyName hg19","$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json"],"flags":{"type":{"name":"type","type":"option","char":"t","description":"type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom"},"assemblyName":{"name":"assemblyName","type":"option","char":"a","description":"Assembly name of the connection If none, will default to the assembly in your config file"},"config":{"name":"config","type":"option","char":"c","description":"Any extra config settings to add to connection in JSON object format, such as '{\"uri\":\"url\":\"https://sample.com\"}, \"locationType\": \"UriLocation\"}'"},"connectionId":{"name":"connectionId","type":"option","description":"Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'"},"name":{"name":"name","type":"option","char":"n","description":"Name of the connection. Defaults to connectionId if not provided"},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to."},"out":{"name":"out","type":"option","description":"synonym for target"},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"skipCheck":{"name":"skipCheck","type":"boolean","description":"Don't check whether or not the data directory URL exists or if you are in a JBrowse directory","allowNo":false},"overwrite":{"name":"overwrite","type":"boolean","description":"Overwrites any existing connections if same connection id","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Equivalent to `--skipCheck --overwrite`","allowNo":false}},"args":[{"name":"connectionUrlOrPath","description":"URL of data directory\nFor hub file, usually called hub.txt\nFor JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ","required":true}]},"add-track-json":{"id":"add-track-json","description":"Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse add-track-json track.json","$ jbrowse add-track-json track.json --update"],"flags":{"update":{"name":"update","type":"boolean","char":"u","description":"update the contents of an existing track, matched based on trackId","allowNo":false},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent"},"out":{"name":"out","type":"option","description":"synonym for target"}},"args":[{"name":"track","description":"track JSON file or command line arg blob","required":true}]},"add-track":{"id":"add-track","description":"Add a track to a JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json","$ jbrowse add-track /path/to/my.bam --load copy","","# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json","$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam","","# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai","$ jbrowse add-track my.bam --indexFile my.bai --load copy","","# creates symlink for /path/to/my.bam and adds track to config.json","$ jbrowse add-track /path/to/my.bam --load symlink","","# add track from URL to config.json, no --load flag needed","$ jbrowse add-track https://mywebsite.com/my.bam","","# --load inPlace adds a track without doing file operations","$ jbrowse add-track /url/relative/path.bam --load inPlace"],"flags":{"trackType":{"name":"trackType","type":"option","char":"t","description":"Type of track, by default inferred from track file"},"name":{"name":"name","type":"option","char":"n","description":"Name of the track. Will be defaulted to the trackId if none specified"},"indexFile":{"name":"indexFile","type":"option","description":"Optional index file for the track"},"description":{"name":"description","type":"option","char":"d","description":"Optional description of the track"},"assemblyNames":{"name":"assemblyNames","type":"option","char":"a","description":"Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file"},"category":{"name":"category","type":"option","description":"Optional Comma separated string of categories to group tracks"},"config":{"name":"config","type":"option","description":"Any extra config settings to add to a track. i.e '{\"defaultRendering\": \"density\"}'"},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation to write out to."},"out":{"name":"out","type":"option","description":"synonym for target"},"subDir":{"name":"subDir","type":"option","description":"when using --load a file, output to a subdirectory of the target dir","default":""},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"trackId":{"name":"trackId","type":"option","description":"trackId for the track, by default inferred from filename, must be unique throughout config"},"load":{"name":"load","type":"option","char":"l","description":"Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone","options":["copy","symlink","move","inPlace"]},"skipCheck":{"name":"skipCheck","type":"boolean","description":"Skip check for whether or not the file or URL exists or if you are in a JBrowse directory","allowNo":false},"overwrite":{"name":"overwrite","type":"boolean","description":"Overwrites existing track if it shares the same trackId","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Equivalent to `--skipCheck --overwrite`","allowNo":false},"protocol":{"name":"protocol","type":"option","description":"Force protocol to a specific value","default":"uri"}},"args":[{"name":"track","description":"Track file or URL","required":true}]},"admin-server":{"id":"admin-server","description":"Start up a small admin server for JBrowse configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse admin-server","$ jbrowse admin-server -p 8888"],"flags":{"port":{"name":"port","type":"option","char":"p","description":"Specifified port to start the server on;\nDefault is 9090."},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent"},"out":{"name":"out","type":"option","description":"synonym for target"},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false}},"args":[]},"create":{"id":"create","description":"Downloads and installs the latest JBrowse 2 release","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# Download latest release from github, and put in specific path","$ jbrowse create /path/to/new/installation","","# Download latest release from github and force overwrite existing contents at path","$ jbrowse create /path/to/new/installation --force","","# Download latest release from a specific URL","$ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip","","# Download a specific tag from github","$ jbrowse create /path/to/new/installation --tag v1.0.0","","# List available versions","$ jbrowse create --listVersions"],"flags":{"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Overwrites existing JBrowse 2 installation if present in path","allowNo":false},"listVersions":{"name":"listVersions","type":"boolean","char":"l","description":"Lists out all versions of JBrowse 2","allowNo":false},"branch":{"name":"branch","type":"option","description":"Download a development build from a named git branch"},"nightly":{"name":"nightly","type":"boolean","description":"Download the latest development build from the main branch","allowNo":false},"url":{"name":"url","type":"option","char":"u","description":"A direct URL to a JBrowse 2 release"},"tag":{"name":"tag","type":"option","char":"t","description":"Version of JBrowse 2 to install. Format is v1.0.0.\nDefaults to latest"}},"args":[{"name":"localPath","description":"Location where JBrowse 2 will be installed","required":true}]},"set-default-session":{"id":"set-default-session","description":"Set a default session with views and tracks","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse set-default-session --session /path/to/default/session.json","$ jbrowse set-default-session --target /path/to/jb2/installation/config.json --view LinearGenomeView --tracks track1, track2, track3","$ jbrowse set-default-session --view LinearGenomeView, --name newName --viewId view-no-tracks","$ jbrowse set-default-session --currentSession # Prints out current default session"],"flags":{"session":{"name":"session","type":"option","char":"s","description":"set path to a file containing session in json format"},"name":{"name":"name","type":"option","char":"n","description":"Give a name for the default session","default":"New Default Session"},"view":{"name":"view","type":"option","char":"v","description":"View type in config to be added as default session, i.e LinearGenomeView, CircularView, DotplotView.\nMust be provided if no default session file provided"},"viewId":{"name":"viewId","type":"option","description":"Identifier for the view. Will be generated on default"},"tracks":{"name":"tracks","type":"option","char":"t","description":"Track id or track ids as comma separated string to put into default session"},"currentSession":{"name":"currentSession","type":"boolean","char":"c","description":"List out the current default session","allowNo":false},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to"},"out":{"name":"out","type":"option","description":"synonym for target"},"delete":{"name":"delete","type":"boolean","description":"Delete any existing default session.","allowNo":false},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false}},"args":[]},"text-index":{"id":"text-index","description":"Make a text-indexing file for any given track(s).","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# indexes all tracks that it can find in the current directory's config.json","$ jbrowse text-index","","# indexes specific trackIds that it can find in the current directory's config.json","$ jbrowse text-index --tracks=track1,track2,track3","","# indexes all tracks in a directory's config.json or in a specific config file","$ jbrowse text-index --out /path/to/jb2/","","# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)","$ jbrowse text-index -a hg19 --force","","# create index for some files for use in @jbrowse/react-linear-genome-view or similar","$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes"],"flags":{"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"tracks":{"name":"tracks","type":"option","description":"Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks"},"target":{"name":"target","type":"option","description":"Path to config file in JB2 installation directory to read from."},"out":{"name":"out","type":"option","description":"Synonym for target"},"attributes":{"name":"attributes","type":"option","description":"Comma separated list of attributes to index","default":"Name,ID"},"assemblies":{"name":"assemblies","type":"option","char":"a","description":"Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config"},"force":{"name":"force","type":"boolean","description":"Overwrite previously existing indexes","allowNo":false},"quiet":{"name":"quiet","type":"boolean","char":"q","description":"Hide the progress bars","allowNo":false},"perTrack":{"name":"perTrack","type":"boolean","description":"If set, creates an index per track","allowNo":false},"exclude":{"name":"exclude","type":"option","description":"Adds gene type to list of excluded types","default":"CDS,exon"},"file":{"name":"file","type":"option","description":"File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)"},"dryrun":{"name":"dryrun","type":"boolean","description":"Just print out tracks that will be indexed by the process, without doing any indexing","allowNo":false}},"args":[]},"upgrade":{"id":"upgrade","description":"Upgrades JBrowse 2 to latest version","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# Upgrades current directory to latest jbrowse release","$ jbrowse upgrade","","# Upgrade jbrowse instance at a specific filesystem path","$ jbrowse upgrade /path/to/jbrowse2/installation","","# Upgrade to a specific tag","$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0","","# List versions available on github","$ jbrowse upgrade --listVersions","","# Upgrade from a specific URL","$ jbrowse upgrade --url https://sample.com/jbrowse2.zip","","# Get nightly release from main branch","$ jbrowse upgrade --nightly"],"flags":{"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"listVersions":{"name":"listVersions","type":"boolean","char":"l","description":"Lists out all versions of JBrowse 2","allowNo":false},"tag":{"name":"tag","type":"option","char":"t","description":"Version of JBrowse 2 to install. Format is v1.0.0.\nDefaults to latest"},"branch":{"name":"branch","type":"option","description":"Download a development build from a named git branch"},"nightly":{"name":"nightly","type":"boolean","description":"Download the latest development build from the main branch","allowNo":false},"url":{"name":"url","type":"option","char":"u","description":"A direct URL to a JBrowse 2 release"}},"args":[{"name":"localPath","description":"Location where JBrowse 2 is installed","required":false,"default":"."}]}}}
1
+ {"version":"1.5.2","commands":{"add-assembly":{"id":"add-assembly","description":"Add an assembly to a JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory","$ jbrowse add-assembly GRCh38.fa --load copy","","# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2","$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy","","# force indexedFasta for add-assembly without relying on file extension","$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy","","# add displayName for an assembly","$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName \"Homo sapiens (hg38)\"","","# use chrom.sizes file for assembly instead of a fasta file","$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace","","# add assembly from preconfigured json file, expert option","$ jbrowse add-assembly GRCh38.config.json --load copy","","# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed","$ jbrowse add-assembly https://example.com/data/sample.2bit","","# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists","$ jbrowse add-assembly myfile.fa.gz --load copy"],"flags":{"type":{"name":"type","type":"option","char":"t","description":"type of sequence, by default inferred from sequence file\n\nindexedFasta An index FASTA (e.g. .fa or .fasta) file;\n can optionally specify --faiLocation\n\nbgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file;\n can optionally specify --faiLocation and/or --gziLocation\n\ntwoBit A twoBit (e.g. .2bit) file\n\nchromSizes A chromosome sizes (e.g. .chrom.sizes) file\n\ncustom Either a JSON file location or inline JSON that defines a custom\n sequence adapter; must provide --name if using inline JSON","options":["indexedFasta","bgzipFasta","twoBit","chromSizes","custom"]},"name":{"name":"name","type":"option","char":"n","description":"Name of the assembly; if not specified, will be guessed using the sequence file name"},"alias":{"name":"alias","type":"option","char":"a","description":"An alias for the assembly name (e.g. \"hg38\" if the name of the assembly is \"GRCh38\");\ncan be specified multiple times"},"displayName":{"name":"displayName","type":"option","description":"The display name to specify for the assembly, e.g. \"Homo sapiens (hg38)\" while the name can be a shorter identifier like \"hg38\""},"faiLocation":{"name":"faiLocation","type":"option","description":"[default: <fastaLocation>.fai] FASTA index file or URL"},"gziLocation":{"name":"gziLocation","type":"option","description":"[default: <fastaLocation>.gzi] FASTA gzip index file or URL"},"refNameAliases":{"name":"refNameAliases","type":"option","description":"Reference sequence name aliases file or URL; assumed to be a tab-separated aliases\nfile unless --refNameAliasesType is specified"},"refNameAliasesType":{"name":"refNameAliasesType","type":"option","description":"Type of aliases defined by --refNameAliases; if \"custom\", --refNameAliases is either\na JSON file location or inline JSON that defines a custom sequence adapter","options":["aliases","custom"]},"refNameColors":{"name":"refNameColors","type":"option","description":"A comma-separated list of color strings for the reference sequence names; will cycle\nthrough colors if there are fewer colors than sequences"},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent"},"out":{"name":"out","type":"option","description":"synonym for target"},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"load":{"name":"load","type":"option","char":"l","description":"Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations","options":["copy","symlink","move","inPlace"]},"skipCheck":{"name":"skipCheck","type":"boolean","description":"Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory","allowNo":false},"overwrite":{"name":"overwrite","type":"boolean","description":"Overwrite existing assembly if one with the same name exists","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Equivalent to `--skipCheck --overwrite`","allowNo":false}},"args":[{"name":"sequence","description":"sequence file or URL\n\nIf TYPE is indexedFasta or bgzipFasta, the index file defaults to <location>.fai\nand can be optionally specified with --faiLocation\nIf TYPE is bgzipFasta, the gzip index file defaults to <location>.gzi and can be\noptionally specified with --gziLocation","required":true}]},"add-connection":{"id":"add-connection","description":"Add a connection to a JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse add-connection http://mysite.com/jbrowse/data/","$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection","$ jbrowse add-connection http://mysite.com/path/to/hub.txt --assemblyName hg19","$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection --assemblyName hg19","$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{\"uri\":{\"url\":\"https://mysite.com/path/to/custom\"}, \"locationType\": \"UriLocation\"}' --assemblyName hg19","$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json"],"flags":{"type":{"name":"type","type":"option","char":"t","description":"type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom"},"assemblyName":{"name":"assemblyName","type":"option","char":"a","description":"Assembly name of the connection If none, will default to the assembly in your config file"},"config":{"name":"config","type":"option","char":"c","description":"Any extra config settings to add to connection in JSON object format, such as '{\"uri\":\"url\":\"https://sample.com\"}, \"locationType\": \"UriLocation\"}'"},"connectionId":{"name":"connectionId","type":"option","description":"Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'"},"name":{"name":"name","type":"option","char":"n","description":"Name of the connection. Defaults to connectionId if not provided"},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to."},"out":{"name":"out","type":"option","description":"synonym for target"},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"skipCheck":{"name":"skipCheck","type":"boolean","description":"Don't check whether or not the data directory URL exists or if you are in a JBrowse directory","allowNo":false},"overwrite":{"name":"overwrite","type":"boolean","description":"Overwrites any existing connections if same connection id","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Equivalent to `--skipCheck --overwrite`","allowNo":false}},"args":[{"name":"connectionUrlOrPath","description":"URL of data directory\nFor hub file, usually called hub.txt\nFor JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ","required":true}]},"add-track-json":{"id":"add-track-json","description":"Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse add-track-json track.json","$ jbrowse add-track-json track.json --update"],"flags":{"update":{"name":"update","type":"boolean","char":"u","description":"update the contents of an existing track, matched based on trackId","allowNo":false},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent"},"out":{"name":"out","type":"option","description":"synonym for target"}},"args":[{"name":"track","description":"track JSON file or command line arg blob","required":true}]},"add-track":{"id":"add-track","description":"Add a track to a JBrowse 2 configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json","$ jbrowse add-track /path/to/my.bam --load copy","","# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json","$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam","","# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai","$ jbrowse add-track my.bam --indexFile my.bai --load copy","","# creates symlink for /path/to/my.bam and adds track to config.json","$ jbrowse add-track /path/to/my.bam --load symlink","","# add track from URL to config.json, no --load flag needed","$ jbrowse add-track https://mywebsite.com/my.bam","","# --load inPlace adds a track without doing file operations","$ jbrowse add-track /url/relative/path.bam --load inPlace"],"flags":{"trackType":{"name":"trackType","type":"option","char":"t","description":"Type of track, by default inferred from track file"},"name":{"name":"name","type":"option","char":"n","description":"Name of the track. Will be defaulted to the trackId if none specified"},"indexFile":{"name":"indexFile","type":"option","description":"Optional index file for the track"},"description":{"name":"description","type":"option","char":"d","description":"Optional description of the track"},"assemblyNames":{"name":"assemblyNames","type":"option","char":"a","description":"Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file"},"category":{"name":"category","type":"option","description":"Optional Comma separated string of categories to group tracks"},"config":{"name":"config","type":"option","description":"Any extra config settings to add to a track. i.e '{\"defaultRendering\": \"density\"}'"},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation to write out to."},"out":{"name":"out","type":"option","description":"synonym for target"},"subDir":{"name":"subDir","type":"option","description":"when using --load a file, output to a subdirectory of the target dir","default":""},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"trackId":{"name":"trackId","type":"option","description":"trackId for the track, by default inferred from filename, must be unique throughout config"},"load":{"name":"load","type":"option","char":"l","description":"Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone","options":["copy","symlink","move","inPlace"]},"skipCheck":{"name":"skipCheck","type":"boolean","description":"Skip check for whether or not the file or URL exists or if you are in a JBrowse directory","allowNo":false},"overwrite":{"name":"overwrite","type":"boolean","description":"Overwrites existing track if it shares the same trackId","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Equivalent to `--skipCheck --overwrite`","allowNo":false},"protocol":{"name":"protocol","type":"option","description":"Force protocol to a specific value","default":"uri"}},"args":[{"name":"track","description":"Track file or URL","required":true}]},"admin-server":{"id":"admin-server","description":"Start up a small admin server for JBrowse configuration","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse admin-server","$ jbrowse admin-server -p 8888"],"flags":{"port":{"name":"port","type":"option","char":"p","description":"Specifified port to start the server on;\nDefault is 9090."},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent"},"out":{"name":"out","type":"option","description":"synonym for target"},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false}},"args":[]},"create":{"id":"create","description":"Downloads and installs the latest JBrowse 2 release","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# Download latest release from github, and put in specific path","$ jbrowse create /path/to/new/installation","","# Download latest release from github and force overwrite existing contents at path","$ jbrowse create /path/to/new/installation --force","","# Download latest release from a specific URL","$ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip","","# Download a specific tag from github","$ jbrowse create /path/to/new/installation --tag v1.0.0","","# List available versions","$ jbrowse create --listVersions"],"flags":{"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"force":{"name":"force","type":"boolean","char":"f","description":"Overwrites existing JBrowse 2 installation if present in path","allowNo":false},"listVersions":{"name":"listVersions","type":"boolean","char":"l","description":"Lists out all versions of JBrowse 2","allowNo":false},"branch":{"name":"branch","type":"option","description":"Download a development build from a named git branch"},"nightly":{"name":"nightly","type":"boolean","description":"Download the latest development build from the main branch","allowNo":false},"url":{"name":"url","type":"option","char":"u","description":"A direct URL to a JBrowse 2 release"},"tag":{"name":"tag","type":"option","char":"t","description":"Version of JBrowse 2 to install. Format is v1.0.0.\nDefaults to latest"}},"args":[{"name":"localPath","description":"Location where JBrowse 2 will be installed","required":true}]},"set-default-session":{"id":"set-default-session","description":"Set a default session with views and tracks","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["$ jbrowse set-default-session --session /path/to/default/session.json","$ jbrowse set-default-session --target /path/to/jb2/installation/config.json --view LinearGenomeView --tracks track1, track2, track3","$ jbrowse set-default-session --view LinearGenomeView, --name newName --viewId view-no-tracks","$ jbrowse set-default-session --currentSession # Prints out current default session"],"flags":{"session":{"name":"session","type":"option","char":"s","description":"set path to a file containing session in json format"},"name":{"name":"name","type":"option","char":"n","description":"Give a name for the default session","default":"New Default Session"},"view":{"name":"view","type":"option","char":"v","description":"View type in config to be added as default session, i.e LinearGenomeView, CircularView, DotplotView.\nMust be provided if no default session file provided"},"viewId":{"name":"viewId","type":"option","description":"Identifier for the view. Will be generated on default"},"tracks":{"name":"tracks","type":"option","char":"t","description":"Track id or track ids as comma separated string to put into default session"},"currentSession":{"name":"currentSession","type":"boolean","char":"c","description":"List out the current default session","allowNo":false},"target":{"name":"target","type":"option","description":"path to config file in JB2 installation directory to write out to"},"out":{"name":"out","type":"option","description":"synonym for target"},"delete":{"name":"delete","type":"boolean","description":"Delete any existing default session.","allowNo":false},"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false}},"args":[]},"text-index":{"id":"text-index","description":"Make a text-indexing file for any given track(s).","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# indexes all tracks that it can find in the current directory's config.json","$ jbrowse text-index","","# indexes specific trackIds that it can find in the current directory's config.json","$ jbrowse text-index --tracks=track1,track2,track3","","# indexes all tracks in a directory's config.json or in a specific config file","$ jbrowse text-index --out /path/to/jb2/","","# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)","$ jbrowse text-index -a hg19 --force","","# create index for some files for use in @jbrowse/react-linear-genome-view or similar","$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes"],"flags":{"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"tracks":{"name":"tracks","type":"option","description":"Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks"},"target":{"name":"target","type":"option","description":"Path to config file in JB2 installation directory to read from."},"out":{"name":"out","type":"option","description":"Synonym for target"},"attributes":{"name":"attributes","type":"option","description":"Comma separated list of attributes to index","default":"Name,ID"},"assemblies":{"name":"assemblies","type":"option","char":"a","description":"Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config"},"force":{"name":"force","type":"boolean","description":"Overwrite previously existing indexes","allowNo":false},"quiet":{"name":"quiet","type":"boolean","char":"q","description":"Hide the progress bars","allowNo":false},"perTrack":{"name":"perTrack","type":"boolean","description":"If set, creates an index per track","allowNo":false},"exclude":{"name":"exclude","type":"option","description":"Adds gene type to list of excluded types","default":"CDS,exon"},"file":{"name":"file","type":"option","description":"File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)"},"dryrun":{"name":"dryrun","type":"boolean","description":"Just print out tracks that will be indexed by the process, without doing any indexing","allowNo":false}},"args":[]},"upgrade":{"id":"upgrade","description":"Upgrades JBrowse 2 to latest version","pluginName":"@jbrowse/cli","pluginType":"core","aliases":[],"examples":["# Upgrades current directory to latest jbrowse release","$ jbrowse upgrade","","# Upgrade jbrowse instance at a specific filesystem path","$ jbrowse upgrade /path/to/jbrowse2/installation","","# Upgrade to a specific tag","$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0","","# List versions available on github","$ jbrowse upgrade --listVersions","","# Upgrade from a specific URL","$ jbrowse upgrade --url https://sample.com/jbrowse2.zip","","# Get nightly release from main branch","$ jbrowse upgrade --nightly"],"flags":{"help":{"name":"help","type":"boolean","char":"h","description":"show CLI help","allowNo":false},"listVersions":{"name":"listVersions","type":"boolean","char":"l","description":"Lists out all versions of JBrowse 2","allowNo":false},"tag":{"name":"tag","type":"option","char":"t","description":"Version of JBrowse 2 to install. Format is v1.0.0.\nDefaults to latest"},"branch":{"name":"branch","type":"option","description":"Download a development build from a named git branch"},"nightly":{"name":"nightly","type":"boolean","description":"Download the latest development build from the main branch","allowNo":false},"url":{"name":"url","type":"option","char":"u","description":"A direct URL to a JBrowse 2 release"}},"args":[{"name":"localPath","description":"Location where JBrowse 2 is installed","required":false,"default":"."}]}}}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/cli",
3
- "version": "1.5.1",
3
+ "version": "1.5.2",
4
4
  "description": "A command line tool for working with JBrowse 2",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -47,6 +47,7 @@
47
47
  "@gmod/gff": "^1.1.2",
48
48
  "@oclif/command": "^1",
49
49
  "@oclif/config": "^1",
50
+ "@oclif/errors": "^1",
50
51
  "@oclif/plugin-help": "^3",
51
52
  "boxen": "^4.2.0",
52
53
  "chalk": "^4.1.0",
@@ -54,7 +55,7 @@
54
55
  "cors": "^2.8.5",
55
56
  "express": "^4.17.1",
56
57
  "follow-redirects": "^1.14.1",
57
- "ixixx": "^1.0.17",
58
+ "ixixx": "^1.0.19",
58
59
  "json-parse-better-errors": "^1.0.2",
59
60
  "node-fetch": "^2.6.0",
60
61
  "object.fromentries": "^2.0.5",
@@ -76,5 +77,5 @@
76
77
  "publishConfig": {
77
78
  "access": "public"
78
79
  },
79
- "gitHead": "284e408c72a3d4d7a0d603197501a8fc8f68c4bc"
80
+ "gitHead": "94fdfbc34787ab8f12a87e00038da74b247b42fa"
80
81
  }