JBrowse2的Monorepo包含JB2产品（网络、桌面、嵌入式），以及核心包和插件.zip

--- title: Command line tools id: cli toplevel: true --- This document covers the CLI tools. Note: for @jbrowse/img static export tool, see https://www.npmjs.com/package/@jbrowse/img Note: the @jbrowse/cli may not do all types of operations, some use cases may best be handled by creating your own tools to manipulate a config.json by hand or by using a script file. A simple script that does not use @jbrowse/cli at all may just look like this ``` const config = JSON.parse(fs.readFileSync('config.json', 'utf8')) // do something with config.tracks, config.assemblies, etc. fs.writeFileSync('config.json', JSON.stringify(config, null, 2)) ``` ## Installation The command line tools can be installed globally using `npm` as follows ```sh-session $ npm install -g @jbrowse/cli ``` A CLI tool called `jbrowse` should then be available in the path. You can test your installation with ```sh-session $ jbrowse --version ``` It is also possible to do one-off executions using npx, e.g. ```sh-session npx @jbrowse/cli create myfolder ``` It is likely preferable in most cases to install the tools globally with `npm install @jbrowse/cli -g` however ## Commands <!-- commands --> - [`jbrowse add-assembly SEQUENCE`](#jbrowse-add-assembly-sequence) - [`jbrowse add-connection CONNECTIONURLORPATH`](#jbrowse-add-connection-connectionurlorpath) - [`jbrowse add-track TRACK`](#jbrowse-add-track-track) - [`jbrowse add-track-json TRACK`](#jbrowse-add-track-json-track) - [`jbrowse admin-server`](#jbrowse-admin-server) - [`jbrowse create LOCALPATH`](#jbrowse-create-localpath) - [`jbrowse help [COMMAND]`](#jbrowse-help-command) - [`jbrowse remove-track TRACK`](#jbrowse-remove-track-track) - [`jbrowse set-default-session`](#jbrowse-set-default-session) - [`jbrowse text-index`](#jbrowse-text-index) - [`jbrowse upgrade [LOCALPATH]`](#jbrowse-upgrade-localpath) ## `jbrowse add-assembly SEQUENCE` Add an assembly to a JBrowse 2 configuration ``` USAGE $ jbrowse add-assembly SEQUENCE ARGUMENTS SEQUENCE sequence file or URL If TYPE is indexedFasta or bgzipFasta, the index file defaults to <location>.fai and can be optionally specified with --faiLocation If TYPE is bgzipFasta, the gzip index file defaults to <location>.gzi and can be optionally specified with --gziLocation OPTIONS -a, --alias=alias An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); can be specified multiple times -f, --force Equivalent to `--skipCheck --overwrite` -h, --help show CLI help -l, --load=copy|symlink|move|inPlace 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 -n, --name=name Name of the assembly; if not specified, will be guessed using the sequence file name -t, --type=indexedFasta|bgzipFasta|twoBit|chromSizes|custom type of sequence, by default inferred from sequence file indexedFasta An index FASTA (e.g. .fa or .fasta) file; can optionally specify --faiLocation bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; can optionally specify --faiLocation and/or --gziLocation twoBit A twoBit (e.g. .2bit) file chromSizes A chromosome sizes (e.g. .chrom.sizes) file custom Either a JSON file location or inline JSON that defines a custom sequence adapter; must provide --name if using inline JSON --displayName=displayName The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38" --faiLocation=faiLocation [default: <fastaLocation>.fai] FASTA index file or URL --gziLocation=gziLocation [default: <fastaLocation>.gzi] FASTA gzip index file or URL --out=out synonym for target --overwrite Overwrite existing assembly if one with the same name exists --refNameAliases=refNameAliases Reference sequence name aliases file or URL; assumed to be a tab-separated aliases file unless --refNameAliasesType is specified --refNameAliasesType=aliases|custom Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either a JSON file location or inline JSON that defines a custom sequence adapter --refNameColors=refNameColors A comma-separated list of color strings for the reference sequence names; will cycle through colors if there are fewer colors than sequences --skipCheck Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory --target=target path to config file in JB2 installation directory to write out to. Creates ./config.json if nonexistent 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 ``` _See code: [src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.4.2/products/jbrowse-cli/src/commands/add-assembly.ts)_ ## `jbrowse add-connection CONNECTIONURLORPATH` Add a connection to a JBrowse 2 configuration ``` USAGE $ jbrowse add-connection CONNECTIONURLORPATH ARGUMENTS CONNECTIONURLORPATH URL of data directory For hub file, usually called hub.txt For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ OPTIONS -a, --assemblyName=assemblyName Assembly name of the connection If none, will default to the assembly in your config file -c, --config=config Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}' -f, --force Equivalent to `--skipCheck --overwrite` -h, --help show CLI help -n, --name=name Name of the connection. Defaults to connectionId if not provided -t, --type=type type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom --connectionId=connectionId Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime' --out=out synonym for target --overwrite Overwrites any existing connections if same connection id --skipCheck Don't check whether or not the data directory URL exists or if you are in a JBrowse directory --target=target path to config file in JB2 installation directory to write out to. EXAMPLES $ jbrows