@jbrowse/cli 2.7.0 → 2.7.1
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.
- package/README.md +10 -10
- package/oclif.manifest.json +533 -390
- package/package.json +3 -2
package/oclif.manifest.json
CHANGED
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@@ -1,14 +1,15 @@
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{
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-
"version": "2.7.0",
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"commands": {
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"add-assembly": {
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"id": "add-assembly",
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"description": "Add an assembly to a JBrowse 2 configuration",
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"strict": true,
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"pluginName": "@jbrowse/cli",
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"pluginAlias": "@jbrowse/cli",
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"pluginType": "core",
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"aliases": [],
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"args": {
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"sequence": {
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"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",
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"name": "sequence",
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"required": true
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}
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},
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"description": "Add an assembly to a JBrowse 2 configuration",
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"examples": [
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"# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory",
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"$ jbrowse add-assembly GRCh38.fa --load copy",
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@@ -36,10 +37,10 @@
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],
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"flags": {
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"type": {
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"name": "type",
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"type": "option",
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"char": "t",
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"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",
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"name": "type",
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"hasDynamicHelp": false,
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"multiple": false,
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"options": [
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"indexedFasta",
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@@ -47,133 +48,153 @@
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"twoBit",
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"chromSizes",
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"custom"
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]
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],
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"type": "option"
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},
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"name": {
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"name": "name",
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"type": "option",
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"char": "n",
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"description": "Name of the assembly; if not specified, will be guessed using the sequence file name",
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"
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"name": "name",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"alias": {
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"name": "alias",
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"type": "option",
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"char": "a",
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"description": "An alias for the assembly name (e.g. \"hg38\" if the name of the assembly is \"GRCh38\");\ncan be specified multiple times",
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"
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"name": "alias",
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"hasDynamicHelp": false,
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"multiple": true,
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"type": "option"
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},
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"displayName": {
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"name": "displayName",
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"type": "option",
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"description": "The display name to specify for the assembly, e.g. \"Homo sapiens (hg38)\" while the name can be a shorter identifier like \"hg38\"",
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"
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"name": "displayName",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"faiLocation": {
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"name": "faiLocation",
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"type": "option",
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"description": "[default: <fastaLocation>.fai] FASTA index file or URL",
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"
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"name": "faiLocation",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"gziLocation": {
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"name": "gziLocation",
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"type": "option",
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"description": "[default: <fastaLocation>.gzi] FASTA gzip index file or URL",
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"
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"name": "gziLocation",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"refNameAliases": {
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"name": "refNameAliases",
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"type": "option",
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"description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases\nfile unless --refNameAliasesType is specified",
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"
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"name": "refNameAliases",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"refNameAliasesType": {
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"
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"dependsOn": [
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"refNameAliases"
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],
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"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",
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"name": "refNameAliasesType",
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"hasDynamicHelp": false,
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"multiple": false,
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"options": [
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"aliases",
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"custom"
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],
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"
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"refNameAliases"
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]
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"type": "option"
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},
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"refNameColors": {
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"name": "refNameColors",
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"type": "option",
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"description": "A comma-separated list of color strings for the reference sequence names; will cycle\nthrough colors if there are fewer colors than sequences",
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"
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"name": "refNameColors",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"target": {
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"name": "target",
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"type": "option",
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"description": "path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent",
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"
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"name": "target",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"out": {
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"name": "out",
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"type": "option",
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"description": "synonym for target",
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"
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"name": "out",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"help": {
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"name": "help",
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"type": "boolean",
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"char": "h",
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"description": "Show CLI help.",
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"
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"name": "help",
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"allowNo": false,
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"type": "boolean"
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},
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"load": {
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"name": "load",
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"type": "option",
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"char": "l",
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"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",
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"name": "load",
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"hasDynamicHelp": false,
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"multiple": false,
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"options": [
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"copy",
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"symlink",
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"move",
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"inPlace"
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]
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],
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"type": "option"
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},
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"skipCheck": {
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"name": "skipCheck",
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"type": "boolean",
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"description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory",
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"
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"name": "skipCheck",
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"allowNo": false,
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"type": "boolean"
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},
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"overwrite": {
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"name": "overwrite",
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"type": "boolean",
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"description": "Overwrite existing assembly if one with the same name exists",
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"
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"name": "overwrite",
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"allowNo": false,
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"type": "boolean"
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},
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"force": {
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"name": "force",
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"type": "boolean",
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"char": "f",
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"description": "Equivalent to `--skipCheck --overwrite`",
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"
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"name": "force",
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"allowNo": false,
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"type": "boolean"
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}
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},
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"hasDynamicHelp": false,
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"hiddenAliases": [],
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"id": "add-assembly",
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"pluginAlias": "@jbrowse/cli",
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"pluginName": "@jbrowse/cli",
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"pluginType": "core",
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"strict": true,
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"isESM": false,
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"relativePath": [
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"lib",
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"commands",
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"add-assembly.js"
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]
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},
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"add-connection": {
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"aliases": [],
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"args": {
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"
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"
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"
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"connectionUrlOrPath": {
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"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/ ",
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"name": "connectionUrlOrPath",
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"required": true
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}
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}
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},
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"add-connection": {
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"id": "add-connection",
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},
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"description": "Add a connection to a JBrowse 2 configuration",
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"strict": true,
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"pluginName": "@jbrowse/cli",
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"pluginAlias": "@jbrowse/cli",
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"pluginType": "core",
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"aliases": [],
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"examples": [
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"$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19",
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"$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38",
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],
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"flags": {
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"type": {
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"name": "type",
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"type": "option",
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"char": "t",
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"description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom",
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"
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"name": "type",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"assemblyNames": {
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"name": "assemblyNames",
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"type": "option",
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"char": "a",
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"description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name",
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"
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"name": "assemblyNames",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"config": {
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"name": "config",
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"type": "option",
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"char": "c",
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"description": "Any extra config settings to add to connection in JSON object format, such as '{\"uri\":\"url\":\"https://sample.com\"}, \"locationType\": \"UriLocation\"}'",
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"
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"name": "config",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"connectionId": {
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"name": "connectionId",
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"type": "option",
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"description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'",
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"
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"name": "connectionId",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"name": {
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"name": "name",
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"type": "option",
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"char": "n",
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"description": "Name of the connection. Defaults to connectionId if not provided",
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"
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"name": "name",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"target": {
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"name": "target",
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"type": "option",
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"description": "path to config file in JB2 installation directory to write out to.",
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"
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"name": "target",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"out": {
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"name": "out",
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"description": "synonym for target",
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"
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"name": "out",
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"hasDynamicHelp": false,
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"multiple": false,
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"type": "option"
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},
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"id": "add-track-json",
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"aliases": [],
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"description": "Track file or URL",
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"id": "add-track",
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"description": "Add a track to a JBrowse 2 configuration",
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"aliases": [],
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"examples": [
|
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|
"# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json",
|
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|
|
@@ -334,194 +380,228 @@
|
|
|
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|
],
|
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|
"flags": {
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"trackType": {
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|
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"name": "trackType",
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"type": "option",
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|
"char": "t",
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|
"description": "Type of track, by default inferred from track file",
|
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|
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"name": "trackType",
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"hasDynamicHelp": false,
|
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|
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"multiple": false,
|
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|
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"type": "option"
|
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},
|
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"name": {
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"name": "name",
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"type": "option",
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"char": "n",
|
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|
"description": "Name of the track. Will be defaulted to the trackId if none specified",
|
|
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"name": "name",
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"hasDynamicHelp": false,
|
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|
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"multiple": false,
|
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"type": "option"
|
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},
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"indexFile": {
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"name": "indexFile",
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"type": "option",
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"description": "Optional index file for the track",
|
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|
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"name": "indexFile",
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"hasDynamicHelp": false,
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|
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"multiple": false,
|
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|
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"type": "option"
|
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|
},
|
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"description": {
|
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|
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"name": "description",
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|
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"type": "option",
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|
"char": "d",
|
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|
"description": "Optional description of the track",
|
|
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|
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|
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|
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"name": "description",
|
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|
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"hasDynamicHelp": false,
|
|
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|
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"multiple": false,
|
|
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|
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"type": "option"
|
|
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|
},
|
|
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|
"assemblyNames": {
|
|
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|
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"name": "assemblyNames",
|
|
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|
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"type": "option",
|
|
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|
"char": "a",
|
|
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415
|
"description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file",
|
|
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|
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"
|
|
416
|
+
"name": "assemblyNames",
|
|
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|
+
"hasDynamicHelp": false,
|
|
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|
+
"multiple": false,
|
|
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|
+
"type": "option"
|
|
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|
},
|
|
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|
"category": {
|
|
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|
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"name": "category",
|
|
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|
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"type": "option",
|
|
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|
"description": "Optional Comma separated string of categories to group tracks",
|
|
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|
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"
|
|
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|
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"name": "category",
|
|
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|
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"hasDynamicHelp": false,
|
|
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|
+
"multiple": false,
|
|
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|
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"type": "option"
|
|
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|
},
|
|
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|
"config": {
|
|
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|
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"name": "config",
|
|
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|
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"type": "option",
|
|
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429
|
"description": "Any extra config settings to add to a track. i.e '{\"defaultRendering\": \"density\"}'",
|
|
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|
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"
|
|
430
|
+
"name": "config",
|
|
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|
+
"hasDynamicHelp": false,
|
|
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|
+
"multiple": false,
|
|
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|
+
"type": "option"
|
|
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|
},
|
|
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|
"target": {
|
|
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|
-
"name": "target",
|
|
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|
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"type": "option",
|
|
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436
|
"description": "path to config file in JB2 installation to write out to.",
|
|
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|
-
"
|
|
437
|
+
"name": "target",
|
|
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|
+
"hasDynamicHelp": false,
|
|
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|
+
"multiple": false,
|
|
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|
+
"type": "option"
|
|
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|
},
|
|
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442
|
"out": {
|
|
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|
-
"name": "out",
|
|
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|
-
"type": "option",
|
|
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443
|
"description": "synonym for target",
|
|
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|
-
"
|
|
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|
+
"name": "out",
|
|
445
|
+
"hasDynamicHelp": false,
|
|
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|
+
"multiple": false,
|
|
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|
+
"type": "option"
|
|
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|
},
|
|
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449
|
"subDir": {
|
|
395
|
-
"name": "subDir",
|
|
396
|
-
"type": "option",
|
|
397
450
|
"description": "when using --load a file, output to a subdirectory of the target dir",
|
|
451
|
+
"name": "subDir",
|
|
452
|
+
"default": "",
|
|
453
|
+
"hasDynamicHelp": false,
|
|
398
454
|
"multiple": false,
|
|
399
|
-
"
|
|
455
|
+
"type": "option"
|
|
400
456
|
},
|
|
401
457
|
"help": {
|
|
402
|
-
"name": "help",
|
|
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|
-
"type": "boolean",
|
|
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458
|
"char": "h",
|
|
405
459
|
"description": "Show CLI help.",
|
|
406
|
-
"
|
|
460
|
+
"name": "help",
|
|
461
|
+
"allowNo": false,
|
|
462
|
+
"type": "boolean"
|
|
407
463
|
},
|
|
408
464
|
"trackId": {
|
|
409
|
-
"name": "trackId",
|
|
410
|
-
"type": "option",
|
|
411
465
|
"description": "trackId for the track, by default inferred from filename, must be unique throughout config",
|
|
412
|
-
"
|
|
466
|
+
"name": "trackId",
|
|
467
|
+
"hasDynamicHelp": false,
|
|
468
|
+
"multiple": false,
|
|
469
|
+
"type": "option"
|
|
413
470
|
},
|
|
414
471
|
"load": {
|
|
415
|
-
"name": "load",
|
|
416
|
-
"type": "option",
|
|
417
472
|
"char": "l",
|
|
418
473
|
"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",
|
|
474
|
+
"name": "load",
|
|
475
|
+
"hasDynamicHelp": false,
|
|
419
476
|
"multiple": false,
|
|
420
477
|
"options": [
|
|
421
478
|
"copy",
|
|
422
479
|
"symlink",
|
|
423
480
|
"move",
|
|
424
481
|
"inPlace"
|
|
425
|
-
]
|
|
482
|
+
],
|
|
483
|
+
"type": "option"
|
|
426
484
|
},
|
|
427
485
|
"skipCheck": {
|
|
428
|
-
"name": "skipCheck",
|
|
429
|
-
"type": "boolean",
|
|
430
486
|
"description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory",
|
|
431
|
-
"
|
|
487
|
+
"name": "skipCheck",
|
|
488
|
+
"allowNo": false,
|
|
489
|
+
"type": "boolean"
|
|
432
490
|
},
|
|
433
491
|
"overwrite": {
|
|
434
|
-
"name": "overwrite",
|
|
435
|
-
"type": "boolean",
|
|
436
492
|
"description": "Overwrites existing track if it shares the same trackId",
|
|
437
|
-
"
|
|
493
|
+
"name": "overwrite",
|
|
494
|
+
"allowNo": false,
|
|
495
|
+
"type": "boolean"
|
|
438
496
|
},
|
|
439
497
|
"force": {
|
|
440
|
-
"name": "force",
|
|
441
|
-
"type": "boolean",
|
|
442
498
|
"char": "f",
|
|
443
499
|
"description": "Equivalent to `--skipCheck --overwrite`",
|
|
444
|
-
"
|
|
500
|
+
"name": "force",
|
|
501
|
+
"allowNo": false,
|
|
502
|
+
"type": "boolean"
|
|
445
503
|
},
|
|
446
504
|
"protocol": {
|
|
447
|
-
"name": "protocol",
|
|
448
|
-
"type": "option",
|
|
449
505
|
"description": "Force protocol to a specific value",
|
|
506
|
+
"name": "protocol",
|
|
507
|
+
"default": "uri",
|
|
508
|
+
"hasDynamicHelp": false,
|
|
450
509
|
"multiple": false,
|
|
451
|
-
"
|
|
510
|
+
"type": "option"
|
|
452
511
|
},
|
|
453
512
|
"bed1": {
|
|
454
|
-
"name": "bed1",
|
|
455
|
-
"type": "option",
|
|
456
513
|
"description": "Used only for mcscan anchors/simpleAnchors types",
|
|
457
|
-
"
|
|
514
|
+
"name": "bed1",
|
|
515
|
+
"hasDynamicHelp": false,
|
|
516
|
+
"multiple": false,
|
|
517
|
+
"type": "option"
|
|
458
518
|
},
|
|
459
519
|
"bed2": {
|
|
460
|
-
"name": "bed2",
|
|
461
|
-
"type": "option",
|
|
462
520
|
"description": "Used only for mcscan anchors/simpleAnchors types",
|
|
463
|
-
"
|
|
521
|
+
"name": "bed2",
|
|
522
|
+
"hasDynamicHelp": false,
|
|
523
|
+
"multiple": false,
|
|
524
|
+
"type": "option"
|
|
464
525
|
}
|
|
465
526
|
},
|
|
466
|
-
"
|
|
467
|
-
|
|
468
|
-
|
|
469
|
-
"description": "Track file or URL",
|
|
470
|
-
"required": true
|
|
471
|
-
}
|
|
472
|
-
}
|
|
473
|
-
},
|
|
474
|
-
"admin-server": {
|
|
475
|
-
"id": "admin-server",
|
|
476
|
-
"description": "Start up a small admin server for JBrowse configuration",
|
|
477
|
-
"strict": true,
|
|
478
|
-
"pluginName": "@jbrowse/cli",
|
|
527
|
+
"hasDynamicHelp": false,
|
|
528
|
+
"hiddenAliases": [],
|
|
529
|
+
"id": "add-track",
|
|
479
530
|
"pluginAlias": "@jbrowse/cli",
|
|
531
|
+
"pluginName": "@jbrowse/cli",
|
|
480
532
|
"pluginType": "core",
|
|
533
|
+
"strict": true,
|
|
534
|
+
"isESM": false,
|
|
535
|
+
"relativePath": [
|
|
536
|
+
"lib",
|
|
537
|
+
"commands",
|
|
538
|
+
"add-track.js"
|
|
539
|
+
]
|
|
540
|
+
},
|
|
541
|
+
"admin-server": {
|
|
481
542
|
"aliases": [],
|
|
543
|
+
"args": {},
|
|
544
|
+
"description": "Start up a small admin server for JBrowse configuration",
|
|
482
545
|
"examples": [
|
|
483
546
|
"$ jbrowse admin-server",
|
|
484
547
|
"$ jbrowse admin-server -p 8888"
|
|
485
548
|
],
|
|
486
549
|
"flags": {
|
|
487
550
|
"port": {
|
|
488
|
-
"name": "port",
|
|
489
|
-
"type": "option",
|
|
490
551
|
"char": "p",
|
|
491
552
|
"description": "Specifified port to start the server on;\nDefault is 9090.",
|
|
492
|
-
"
|
|
553
|
+
"name": "port",
|
|
554
|
+
"hasDynamicHelp": false,
|
|
555
|
+
"multiple": false,
|
|
556
|
+
"type": "option"
|
|
493
557
|
},
|
|
494
558
|
"root": {
|
|
495
|
-
"name": "root",
|
|
496
|
-
"type": "option",
|
|
497
559
|
"description": "path to the root of the JB2 installation.\nCreates ./config.json if nonexistent. note that you can navigate to ?config=path/to/subconfig.json in the web browser and it will write to rootDir/path/to/subconfig.json",
|
|
498
|
-
"
|
|
560
|
+
"name": "root",
|
|
561
|
+
"hasDynamicHelp": false,
|
|
562
|
+
"multiple": false,
|
|
563
|
+
"type": "option"
|
|
499
564
|
},
|
|
500
565
|
"bodySizeLimit": {
|
|
501
|
-
"name": "bodySizeLimit",
|
|
502
|
-
"type": "option",
|
|
503
566
|
"description": "Size limit of the update message; may need to increase if config is large.\nArgument is passed to bytes library for parsing: https://www.npmjs.com/package/bytes.",
|
|
567
|
+
"name": "bodySizeLimit",
|
|
568
|
+
"default": "25mb",
|
|
569
|
+
"hasDynamicHelp": false,
|
|
504
570
|
"multiple": false,
|
|
505
|
-
"
|
|
571
|
+
"type": "option"
|
|
506
572
|
},
|
|
507
573
|
"help": {
|
|
508
|
-
"name": "help",
|
|
509
|
-
"type": "boolean",
|
|
510
574
|
"char": "h",
|
|
511
575
|
"description": "Show CLI help.",
|
|
512
|
-
"
|
|
576
|
+
"name": "help",
|
|
577
|
+
"allowNo": false,
|
|
578
|
+
"type": "boolean"
|
|
513
579
|
}
|
|
514
580
|
},
|
|
515
|
-
"
|
|
516
|
-
|
|
517
|
-
|
|
518
|
-
"id": "create",
|
|
519
|
-
"description": "Downloads and installs the latest JBrowse 2 release",
|
|
520
|
-
"strict": true,
|
|
521
|
-
"pluginName": "@jbrowse/cli",
|
|
581
|
+
"hasDynamicHelp": false,
|
|
582
|
+
"hiddenAliases": [],
|
|
583
|
+
"id": "admin-server",
|
|
522
584
|
"pluginAlias": "@jbrowse/cli",
|
|
585
|
+
"pluginName": "@jbrowse/cli",
|
|
523
586
|
"pluginType": "core",
|
|
587
|
+
"strict": true,
|
|
588
|
+
"isESM": false,
|
|
589
|
+
"relativePath": [
|
|
590
|
+
"lib",
|
|
591
|
+
"commands",
|
|
592
|
+
"admin-server.js"
|
|
593
|
+
]
|
|
594
|
+
},
|
|
595
|
+
"create": {
|
|
524
596
|
"aliases": [],
|
|
597
|
+
"args": {
|
|
598
|
+
"localPath": {
|
|
599
|
+
"description": "Location where JBrowse 2 will be installed",
|
|
600
|
+
"name": "localPath",
|
|
601
|
+
"required": true
|
|
602
|
+
}
|
|
603
|
+
},
|
|
604
|
+
"description": "Downloads and installs the latest JBrowse 2 release",
|
|
525
605
|
"examples": [
|
|
526
606
|
"# Download latest release from github, and put in specific path",
|
|
527
607
|
"$ jbrowse create /path/to/new/installation",
|
|
@@ -540,102 +620,117 @@
|
|
|
540
620
|
],
|
|
541
621
|
"flags": {
|
|
542
622
|
"help": {
|
|
543
|
-
"name": "help",
|
|
544
|
-
"type": "boolean",
|
|
545
623
|
"char": "h",
|
|
546
624
|
"description": "Show CLI help.",
|
|
547
|
-
"
|
|
625
|
+
"name": "help",
|
|
626
|
+
"allowNo": false,
|
|
627
|
+
"type": "boolean"
|
|
548
628
|
},
|
|
549
629
|
"force": {
|
|
550
|
-
"name": "force",
|
|
551
|
-
"type": "boolean",
|
|
552
630
|
"char": "f",
|
|
553
631
|
"description": "Overwrites existing JBrowse 2 installation if present in path",
|
|
554
|
-
"
|
|
632
|
+
"name": "force",
|
|
633
|
+
"allowNo": false,
|
|
634
|
+
"type": "boolean"
|
|
555
635
|
},
|
|
556
636
|
"listVersions": {
|
|
557
|
-
"name": "listVersions",
|
|
558
|
-
"type": "boolean",
|
|
559
637
|
"char": "l",
|
|
560
638
|
"description": "Lists out all versions of JBrowse 2",
|
|
561
|
-
"
|
|
639
|
+
"name": "listVersions",
|
|
640
|
+
"allowNo": false,
|
|
641
|
+
"type": "boolean"
|
|
562
642
|
},
|
|
563
643
|
"branch": {
|
|
564
|
-
"name": "branch",
|
|
565
|
-
"type": "option",
|
|
566
644
|
"description": "Download a development build from a named git branch",
|
|
567
|
-
"
|
|
645
|
+
"name": "branch",
|
|
646
|
+
"hasDynamicHelp": false,
|
|
647
|
+
"multiple": false,
|
|
648
|
+
"type": "option"
|
|
568
649
|
},
|
|
569
650
|
"nightly": {
|
|
570
|
-
"name": "nightly",
|
|
571
|
-
"type": "boolean",
|
|
572
651
|
"description": "Download the latest development build from the main branch",
|
|
573
|
-
"
|
|
652
|
+
"name": "nightly",
|
|
653
|
+
"allowNo": false,
|
|
654
|
+
"type": "boolean"
|
|
574
655
|
},
|
|
575
656
|
"url": {
|
|
576
|
-
"name": "url",
|
|
577
|
-
"type": "option",
|
|
578
657
|
"char": "u",
|
|
579
658
|
"description": "A direct URL to a JBrowse 2 release",
|
|
580
|
-
"
|
|
659
|
+
"name": "url",
|
|
660
|
+
"hasDynamicHelp": false,
|
|
661
|
+
"multiple": false,
|
|
662
|
+
"type": "option"
|
|
581
663
|
},
|
|
582
664
|
"tag": {
|
|
583
|
-
"name": "tag",
|
|
584
|
-
"type": "option",
|
|
585
665
|
"char": "t",
|
|
586
666
|
"description": "Version of JBrowse 2 to install. Format is v1.0.0.\nDefaults to latest",
|
|
587
|
-
"
|
|
667
|
+
"name": "tag",
|
|
668
|
+
"hasDynamicHelp": false,
|
|
669
|
+
"multiple": false,
|
|
670
|
+
"type": "option"
|
|
588
671
|
}
|
|
589
672
|
},
|
|
673
|
+
"hasDynamicHelp": false,
|
|
674
|
+
"hiddenAliases": [],
|
|
675
|
+
"id": "create",
|
|
676
|
+
"pluginAlias": "@jbrowse/cli",
|
|
677
|
+
"pluginName": "@jbrowse/cli",
|
|
678
|
+
"pluginType": "core",
|
|
679
|
+
"strict": true,
|
|
680
|
+
"isESM": false,
|
|
681
|
+
"relativePath": [
|
|
682
|
+
"lib",
|
|
683
|
+
"commands",
|
|
684
|
+
"create.js"
|
|
685
|
+
]
|
|
686
|
+
},
|
|
687
|
+
"remove-track": {
|
|
688
|
+
"aliases": [],
|
|
590
689
|
"args": {
|
|
591
|
-
"
|
|
592
|
-
"
|
|
593
|
-
"
|
|
690
|
+
"track": {
|
|
691
|
+
"description": "track JSON file or command line arg blob",
|
|
692
|
+
"name": "track",
|
|
594
693
|
"required": true
|
|
595
694
|
}
|
|
596
|
-
}
|
|
597
|
-
},
|
|
598
|
-
"remove-track": {
|
|
599
|
-
"id": "remove-track",
|
|
695
|
+
},
|
|
600
696
|
"description": "Remove a track configuration from a JBrowse 2 configuration. Be aware that this can cause crashes in saved sessions that refer to this track!",
|
|
601
|
-
"strict": true,
|
|
602
|
-
"pluginName": "@jbrowse/cli",
|
|
603
|
-
"pluginAlias": "@jbrowse/cli",
|
|
604
|
-
"pluginType": "core",
|
|
605
|
-
"aliases": [],
|
|
606
697
|
"examples": [
|
|
607
698
|
"$ jbrowse remove-track-json trackId"
|
|
608
699
|
],
|
|
609
700
|
"flags": {
|
|
610
701
|
"target": {
|
|
611
|
-
"name": "target",
|
|
612
|
-
"type": "option",
|
|
613
702
|
"description": "path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent",
|
|
614
|
-
"
|
|
703
|
+
"name": "target",
|
|
704
|
+
"hasDynamicHelp": false,
|
|
705
|
+
"multiple": false,
|
|
706
|
+
"type": "option"
|
|
615
707
|
},
|
|
616
708
|
"out": {
|
|
617
|
-
"name": "out",
|
|
618
|
-
"type": "option",
|
|
619
709
|
"description": "synonym for target",
|
|
620
|
-
"
|
|
710
|
+
"name": "out",
|
|
711
|
+
"hasDynamicHelp": false,
|
|
712
|
+
"multiple": false,
|
|
713
|
+
"type": "option"
|
|
621
714
|
}
|
|
622
715
|
},
|
|
623
|
-
"
|
|
624
|
-
|
|
625
|
-
|
|
626
|
-
"description": "track JSON file or command line arg blob",
|
|
627
|
-
"required": true
|
|
628
|
-
}
|
|
629
|
-
}
|
|
630
|
-
},
|
|
631
|
-
"set-default-session": {
|
|
632
|
-
"id": "set-default-session",
|
|
633
|
-
"description": "Set a default session with views and tracks",
|
|
634
|
-
"strict": true,
|
|
635
|
-
"pluginName": "@jbrowse/cli",
|
|
716
|
+
"hasDynamicHelp": false,
|
|
717
|
+
"hiddenAliases": [],
|
|
718
|
+
"id": "remove-track",
|
|
636
719
|
"pluginAlias": "@jbrowse/cli",
|
|
720
|
+
"pluginName": "@jbrowse/cli",
|
|
637
721
|
"pluginType": "core",
|
|
722
|
+
"strict": true,
|
|
723
|
+
"isESM": false,
|
|
724
|
+
"relativePath": [
|
|
725
|
+
"lib",
|
|
726
|
+
"commands",
|
|
727
|
+
"remove-track.js"
|
|
728
|
+
]
|
|
729
|
+
},
|
|
730
|
+
"set-default-session": {
|
|
638
731
|
"aliases": [],
|
|
732
|
+
"args": {},
|
|
733
|
+
"description": "Set a default session with views and tracks",
|
|
639
734
|
"examples": [
|
|
640
735
|
"$ jbrowse set-default-session --session /path/to/default/session.json",
|
|
641
736
|
"$ jbrowse set-default-session --target /path/to/jb2/installation/config.json --view LinearGenomeView --tracks track1, track2, track3",
|
|
@@ -644,83 +739,98 @@
|
|
|
644
739
|
],
|
|
645
740
|
"flags": {
|
|
646
741
|
"session": {
|
|
647
|
-
"name": "session",
|
|
648
|
-
"type": "option",
|
|
649
742
|
"char": "s",
|
|
650
743
|
"description": "set path to a file containing session in json format",
|
|
651
|
-
"
|
|
744
|
+
"name": "session",
|
|
745
|
+
"hasDynamicHelp": false,
|
|
746
|
+
"multiple": false,
|
|
747
|
+
"type": "option"
|
|
652
748
|
},
|
|
653
749
|
"name": {
|
|
654
|
-
"name": "name",
|
|
655
|
-
"type": "option",
|
|
656
750
|
"char": "n",
|
|
657
751
|
"description": "Give a name for the default session",
|
|
752
|
+
"name": "name",
|
|
753
|
+
"default": "New Default Session",
|
|
754
|
+
"hasDynamicHelp": false,
|
|
658
755
|
"multiple": false,
|
|
659
|
-
"
|
|
756
|
+
"type": "option"
|
|
660
757
|
},
|
|
661
758
|
"view": {
|
|
662
|
-
"name": "view",
|
|
663
|
-
"type": "option",
|
|
664
759
|
"char": "v",
|
|
665
760
|
"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",
|
|
666
|
-
"
|
|
761
|
+
"name": "view",
|
|
762
|
+
"hasDynamicHelp": false,
|
|
763
|
+
"multiple": false,
|
|
764
|
+
"type": "option"
|
|
667
765
|
},
|
|
668
766
|
"viewId": {
|
|
669
|
-
"name": "viewId",
|
|
670
|
-
"type": "option",
|
|
671
767
|
"description": "Identifier for the view. Will be generated on default",
|
|
672
|
-
"
|
|
768
|
+
"name": "viewId",
|
|
769
|
+
"hasDynamicHelp": false,
|
|
770
|
+
"multiple": false,
|
|
771
|
+
"type": "option"
|
|
673
772
|
},
|
|
674
773
|
"tracks": {
|
|
675
|
-
"name": "tracks",
|
|
676
|
-
"type": "option",
|
|
677
774
|
"char": "t",
|
|
678
775
|
"description": "Track id or track ids as comma separated string to put into default session",
|
|
679
|
-
"
|
|
776
|
+
"name": "tracks",
|
|
777
|
+
"hasDynamicHelp": false,
|
|
778
|
+
"multiple": false,
|
|
779
|
+
"type": "option"
|
|
680
780
|
},
|
|
681
781
|
"currentSession": {
|
|
682
|
-
"name": "currentSession",
|
|
683
|
-
"type": "boolean",
|
|
684
782
|
"char": "c",
|
|
685
783
|
"description": "List out the current default session",
|
|
686
|
-
"
|
|
784
|
+
"name": "currentSession",
|
|
785
|
+
"allowNo": false,
|
|
786
|
+
"type": "boolean"
|
|
687
787
|
},
|
|
688
788
|
"target": {
|
|
689
|
-
"name": "target",
|
|
690
|
-
"type": "option",
|
|
691
789
|
"description": "path to config file in JB2 installation directory to write out to",
|
|
692
|
-
"
|
|
790
|
+
"name": "target",
|
|
791
|
+
"hasDynamicHelp": false,
|
|
792
|
+
"multiple": false,
|
|
793
|
+
"type": "option"
|
|
693
794
|
},
|
|
694
795
|
"out": {
|
|
695
|
-
"name": "out",
|
|
696
|
-
"type": "option",
|
|
697
796
|
"description": "synonym for target",
|
|
698
|
-
"
|
|
797
|
+
"name": "out",
|
|
798
|
+
"hasDynamicHelp": false,
|
|
799
|
+
"multiple": false,
|
|
800
|
+
"type": "option"
|
|
699
801
|
},
|
|
700
802
|
"delete": {
|
|
701
|
-
"name": "delete",
|
|
702
|
-
"type": "boolean",
|
|
703
803
|
"description": "Delete any existing default session.",
|
|
704
|
-
"
|
|
804
|
+
"name": "delete",
|
|
805
|
+
"allowNo": false,
|
|
806
|
+
"type": "boolean"
|
|
705
807
|
},
|
|
706
808
|
"help": {
|
|
707
|
-
"name": "help",
|
|
708
|
-
"type": "boolean",
|
|
709
809
|
"char": "h",
|
|
710
810
|
"description": "Show CLI help.",
|
|
711
|
-
"
|
|
811
|
+
"name": "help",
|
|
812
|
+
"allowNo": false,
|
|
813
|
+
"type": "boolean"
|
|
712
814
|
}
|
|
713
815
|
},
|
|
714
|
-
"
|
|
715
|
-
|
|
716
|
-
|
|
717
|
-
"id": "text-index",
|
|
718
|
-
"description": "Make a text-indexing file for any given track(s).",
|
|
719
|
-
"strict": true,
|
|
720
|
-
"pluginName": "@jbrowse/cli",
|
|
816
|
+
"hasDynamicHelp": false,
|
|
817
|
+
"hiddenAliases": [],
|
|
818
|
+
"id": "set-default-session",
|
|
721
819
|
"pluginAlias": "@jbrowse/cli",
|
|
820
|
+
"pluginName": "@jbrowse/cli",
|
|
722
821
|
"pluginType": "core",
|
|
822
|
+
"strict": true,
|
|
823
|
+
"isESM": false,
|
|
824
|
+
"relativePath": [
|
|
825
|
+
"lib",
|
|
826
|
+
"commands",
|
|
827
|
+
"set-default-session.js"
|
|
828
|
+
]
|
|
829
|
+
},
|
|
830
|
+
"text-index": {
|
|
723
831
|
"aliases": [],
|
|
832
|
+
"args": {},
|
|
833
|
+
"description": "Make a text-indexing file for any given track(s).",
|
|
724
834
|
"examples": [
|
|
725
835
|
"# indexes all tracks that it can find in the current directory's config.json",
|
|
726
836
|
"$ jbrowse text-index",
|
|
@@ -739,105 +849,129 @@
|
|
|
739
849
|
],
|
|
740
850
|
"flags": {
|
|
741
851
|
"help": {
|
|
742
|
-
"name": "help",
|
|
743
|
-
"type": "boolean",
|
|
744
852
|
"char": "h",
|
|
745
853
|
"description": "Show CLI help.",
|
|
746
|
-
"
|
|
854
|
+
"name": "help",
|
|
855
|
+
"allowNo": false,
|
|
856
|
+
"type": "boolean"
|
|
747
857
|
},
|
|
748
858
|
"tracks": {
|
|
749
|
-
"name": "tracks",
|
|
750
|
-
"type": "option",
|
|
751
859
|
"description": "Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks",
|
|
752
|
-
"
|
|
860
|
+
"name": "tracks",
|
|
861
|
+
"hasDynamicHelp": false,
|
|
862
|
+
"multiple": false,
|
|
863
|
+
"type": "option"
|
|
753
864
|
},
|
|
754
865
|
"target": {
|
|
755
|
-
"name": "target",
|
|
756
|
-
"type": "option",
|
|
757
866
|
"description": "Path to config file in JB2 installation directory to read from.",
|
|
758
|
-
"
|
|
867
|
+
"name": "target",
|
|
868
|
+
"hasDynamicHelp": false,
|
|
869
|
+
"multiple": false,
|
|
870
|
+
"type": "option"
|
|
759
871
|
},
|
|
760
872
|
"out": {
|
|
761
|
-
"name": "out",
|
|
762
|
-
"type": "option",
|
|
763
873
|
"description": "Synonym for target",
|
|
764
|
-
"
|
|
874
|
+
"name": "out",
|
|
875
|
+
"hasDynamicHelp": false,
|
|
876
|
+
"multiple": false,
|
|
877
|
+
"type": "option"
|
|
765
878
|
},
|
|
766
879
|
"attributes": {
|
|
767
|
-
"name": "attributes",
|
|
768
|
-
"type": "option",
|
|
769
880
|
"description": "Comma separated list of attributes to index",
|
|
881
|
+
"name": "attributes",
|
|
882
|
+
"default": "Name,ID",
|
|
883
|
+
"hasDynamicHelp": false,
|
|
770
884
|
"multiple": false,
|
|
771
|
-
"
|
|
885
|
+
"type": "option"
|
|
772
886
|
},
|
|
773
887
|
"assemblies": {
|
|
774
|
-
"name": "assemblies",
|
|
775
|
-
"type": "option",
|
|
776
888
|
"char": "a",
|
|
777
889
|
"description": "Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config",
|
|
778
|
-
"
|
|
890
|
+
"name": "assemblies",
|
|
891
|
+
"hasDynamicHelp": false,
|
|
892
|
+
"multiple": false,
|
|
893
|
+
"type": "option"
|
|
779
894
|
},
|
|
780
895
|
"force": {
|
|
781
|
-
"name": "force",
|
|
782
|
-
"type": "boolean",
|
|
783
896
|
"description": "Overwrite previously existing indexes",
|
|
784
|
-
"
|
|
897
|
+
"name": "force",
|
|
898
|
+
"allowNo": false,
|
|
899
|
+
"type": "boolean"
|
|
785
900
|
},
|
|
786
901
|
"quiet": {
|
|
787
|
-
"name": "quiet",
|
|
788
|
-
"type": "boolean",
|
|
789
902
|
"char": "q",
|
|
790
903
|
"description": "Hide the progress bars",
|
|
791
|
-
"
|
|
904
|
+
"name": "quiet",
|
|
905
|
+
"allowNo": false,
|
|
906
|
+
"type": "boolean"
|
|
792
907
|
},
|
|
793
908
|
"perTrack": {
|
|
794
|
-
"name": "perTrack",
|
|
795
|
-
"type": "boolean",
|
|
796
909
|
"description": "If set, creates an index per track",
|
|
797
|
-
"
|
|
910
|
+
"name": "perTrack",
|
|
911
|
+
"allowNo": false,
|
|
912
|
+
"type": "boolean"
|
|
798
913
|
},
|
|
799
914
|
"exclude": {
|
|
800
|
-
"name": "exclude",
|
|
801
|
-
"type": "option",
|
|
802
915
|
"description": "Adds gene type to list of excluded types",
|
|
916
|
+
"name": "exclude",
|
|
917
|
+
"default": "CDS,exon",
|
|
918
|
+
"hasDynamicHelp": false,
|
|
803
919
|
"multiple": false,
|
|
804
|
-
"
|
|
920
|
+
"type": "option"
|
|
805
921
|
},
|
|
806
922
|
"prefixSize": {
|
|
807
|
-
"name": "prefixSize",
|
|
808
|
-
"type": "option",
|
|
809
923
|
"description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins",
|
|
810
|
-
"
|
|
924
|
+
"name": "prefixSize",
|
|
925
|
+
"hasDynamicHelp": false,
|
|
926
|
+
"multiple": false,
|
|
927
|
+
"type": "option"
|
|
811
928
|
},
|
|
812
929
|
"file": {
|
|
813
|
-
"name": "file",
|
|
814
|
-
"type": "option",
|
|
815
930
|
"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)",
|
|
816
|
-
"
|
|
931
|
+
"name": "file",
|
|
932
|
+
"hasDynamicHelp": false,
|
|
933
|
+
"multiple": true,
|
|
934
|
+
"type": "option"
|
|
817
935
|
},
|
|
818
936
|
"fileId": {
|
|
819
|
-
"name": "fileId",
|
|
820
|
-
"type": "option",
|
|
821
937
|
"description": "Set the trackId used for the indexes generated with the --file argument",
|
|
822
|
-
"
|
|
938
|
+
"name": "fileId",
|
|
939
|
+
"hasDynamicHelp": false,
|
|
940
|
+
"multiple": true,
|
|
941
|
+
"type": "option"
|
|
823
942
|
},
|
|
824
943
|
"dryrun": {
|
|
825
|
-
"name": "dryrun",
|
|
826
|
-
"type": "boolean",
|
|
827
944
|
"description": "Just print out tracks that will be indexed by the process, without doing any indexing",
|
|
828
|
-
"
|
|
945
|
+
"name": "dryrun",
|
|
946
|
+
"allowNo": false,
|
|
947
|
+
"type": "boolean"
|
|
829
948
|
}
|
|
830
949
|
},
|
|
831
|
-
"
|
|
832
|
-
|
|
833
|
-
|
|
834
|
-
"id": "upgrade",
|
|
835
|
-
"description": "Upgrades JBrowse 2 to latest version",
|
|
836
|
-
"strict": true,
|
|
837
|
-
"pluginName": "@jbrowse/cli",
|
|
950
|
+
"hasDynamicHelp": false,
|
|
951
|
+
"hiddenAliases": [],
|
|
952
|
+
"id": "text-index",
|
|
838
953
|
"pluginAlias": "@jbrowse/cli",
|
|
954
|
+
"pluginName": "@jbrowse/cli",
|
|
839
955
|
"pluginType": "core",
|
|
956
|
+
"strict": true,
|
|
957
|
+
"isESM": false,
|
|
958
|
+
"relativePath": [
|
|
959
|
+
"lib",
|
|
960
|
+
"commands",
|
|
961
|
+
"text-index.js"
|
|
962
|
+
]
|
|
963
|
+
},
|
|
964
|
+
"upgrade": {
|
|
840
965
|
"aliases": [],
|
|
966
|
+
"args": {
|
|
967
|
+
"localPath": {
|
|
968
|
+
"default": ".",
|
|
969
|
+
"description": "Location where JBrowse 2 is installed",
|
|
970
|
+
"name": "localPath",
|
|
971
|
+
"required": false
|
|
972
|
+
}
|
|
973
|
+
},
|
|
974
|
+
"description": "Upgrades JBrowse 2 to latest version",
|
|
841
975
|
"examples": [
|
|
842
976
|
"# Upgrades current directory to latest jbrowse release",
|
|
843
977
|
"$ jbrowse upgrade",
|
|
@@ -859,60 +993,69 @@
|
|
|
859
993
|
],
|
|
860
994
|
"flags": {
|
|
861
995
|
"help": {
|
|
862
|
-
"name": "help",
|
|
863
|
-
"type": "boolean",
|
|
864
996
|
"char": "h",
|
|
865
997
|
"description": "Show CLI help.",
|
|
866
|
-
"
|
|
998
|
+
"name": "help",
|
|
999
|
+
"allowNo": false,
|
|
1000
|
+
"type": "boolean"
|
|
867
1001
|
},
|
|
868
1002
|
"listVersions": {
|
|
869
|
-
"name": "listVersions",
|
|
870
|
-
"type": "boolean",
|
|
871
1003
|
"char": "l",
|
|
872
1004
|
"description": "Lists out all versions of JBrowse 2",
|
|
873
|
-
"
|
|
1005
|
+
"name": "listVersions",
|
|
1006
|
+
"allowNo": false,
|
|
1007
|
+
"type": "boolean"
|
|
874
1008
|
},
|
|
875
1009
|
"tag": {
|
|
876
|
-
"name": "tag",
|
|
877
|
-
"type": "option",
|
|
878
1010
|
"char": "t",
|
|
879
1011
|
"description": "Version of JBrowse 2 to install. Format is v1.0.0.\nDefaults to latest",
|
|
880
|
-
"
|
|
1012
|
+
"name": "tag",
|
|
1013
|
+
"hasDynamicHelp": false,
|
|
1014
|
+
"multiple": false,
|
|
1015
|
+
"type": "option"
|
|
881
1016
|
},
|
|
882
1017
|
"branch": {
|
|
883
|
-
"name": "branch",
|
|
884
|
-
"type": "option",
|
|
885
1018
|
"description": "Download a development build from a named git branch",
|
|
886
|
-
"
|
|
1019
|
+
"name": "branch",
|
|
1020
|
+
"hasDynamicHelp": false,
|
|
1021
|
+
"multiple": false,
|
|
1022
|
+
"type": "option"
|
|
887
1023
|
},
|
|
888
1024
|
"nightly": {
|
|
889
|
-
"name": "nightly",
|
|
890
|
-
"type": "boolean",
|
|
891
1025
|
"description": "Download the latest development build from the main branch",
|
|
892
|
-
"
|
|
1026
|
+
"name": "nightly",
|
|
1027
|
+
"allowNo": false,
|
|
1028
|
+
"type": "boolean"
|
|
893
1029
|
},
|
|
894
1030
|
"clean": {
|
|
895
|
-
"name": "clean",
|
|
896
|
-
"type": "boolean",
|
|
897
1031
|
"description": "Removes old js,map,and LICENSE files in the installation",
|
|
898
|
-
"
|
|
1032
|
+
"name": "clean",
|
|
1033
|
+
"allowNo": false,
|
|
1034
|
+
"type": "boolean"
|
|
899
1035
|
},
|
|
900
1036
|
"url": {
|
|
901
|
-
"name": "url",
|
|
902
|
-
"type": "option",
|
|
903
1037
|
"char": "u",
|
|
904
1038
|
"description": "A direct URL to a JBrowse 2 release",
|
|
905
|
-
"
|
|
1039
|
+
"name": "url",
|
|
1040
|
+
"hasDynamicHelp": false,
|
|
1041
|
+
"multiple": false,
|
|
1042
|
+
"type": "option"
|
|
906
1043
|
}
|
|
907
1044
|
},
|
|
908
|
-
"
|
|
909
|
-
|
|
910
|
-
|
|
911
|
-
|
|
912
|
-
|
|
913
|
-
|
|
914
|
-
|
|
915
|
-
|
|
1045
|
+
"hasDynamicHelp": false,
|
|
1046
|
+
"hiddenAliases": [],
|
|
1047
|
+
"id": "upgrade",
|
|
1048
|
+
"pluginAlias": "@jbrowse/cli",
|
|
1049
|
+
"pluginName": "@jbrowse/cli",
|
|
1050
|
+
"pluginType": "core",
|
|
1051
|
+
"strict": true,
|
|
1052
|
+
"isESM": false,
|
|
1053
|
+
"relativePath": [
|
|
1054
|
+
"lib",
|
|
1055
|
+
"commands",
|
|
1056
|
+
"upgrade.js"
|
|
1057
|
+
]
|
|
916
1058
|
}
|
|
917
|
-
}
|
|
1059
|
+
},
|
|
1060
|
+
"version": "2.7.1"
|
|
918
1061
|
}
|