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    @gmod/jbrowse-cli
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    0.0.1-beta.23 • Public • Published

    title: Command line tools id: cli

    This document covers the CLI tools.

    Installation

    The command line tools can be installed using npm as follows

    $ npm install -g @gmod/jbrowse-cli

    You can test your installation with

    $ jbrowse --version

    It is also possible to do one-off executions using npx, e.g.

    npx @gmod/jbrowse-cli create myfolder

    It is likely preferable in most cases to install the tools first however

    Commands

    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|trust
          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 trust 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
    
      --faiLocation=faiLocation
          [default: <fastaLocation>.fai] FASTA index file or URL
    
      --gziLocation=gziLocation
          [default: <fastaLocation>.gzi] FASTA gzip index file or URL
    
      --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
          [default: ./config.json] path to config file in JB2 installation directory to write out to.
          Creates ./config.json if nonexistent
    
    EXAMPLES
      $ jbrowse add-assembly GRCh38.fa --load copy
      $ jbrowse add-assembly GRCh38.fasta.with.custom.extension.xyz --type indexedFasta --load move
      $ jbrowse add-assembly myFile.fa.gz --name GRCh38 --alias hg38 --load trust
      $ jbrowse add-assembly GRCh38.chrom.sizes --load trust
      $ jbrowse add-assembly GRCh38.config.json --load copy
      $ jbrowse add-assembly https://example.com/data/sample.2bit
      $ jbrowse add-assembly GRCh38.fa --target /path/to/jb2/installation/customconfig.json --load copy
    

    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"}}'
    
      -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'
    
      --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                  [default: ./config.json] path to config file in JB2 installation directory to write
                                       out to.
    
    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"}}' --assemblyName hg19
      $ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target 
      /path/to/jb2/installation/config.json
    

    jbrowse add-track TRACK

    Add a track to a JBrowse 2 configuration

    USAGE
      $ jbrowse add-track TRACK
    
    ARGUMENTS
      TRACK  Track file or URL
    
    OPTIONS
      -a, --assemblyNames=assemblyNames   Assembly name or names for track as comma separated string. If none, will default
                                          to the assembly in your config file
    
      -d, --description=description       Optional description of the track
    
      -f, --force                         Equivalent to `--skipCheck --overwrite`
    
      -h, --help                          show CLI help
    
      -l, --load=copy|symlink|move|trust  Required flag when using a local file. Choose how to manage the track. Copy,
                                          symlink, or move the track to the JBrowse directory. Or trust to leave track alone
    
      -n, --name=name                     Name of the track. Will be defaulted to the trackId if none specified
    
      -t, --type=type                     Type of track, by default inferred from track file
    
      --category=category                 Optional Comma separated string of categories to group tracks
    
      --config=config                     Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'
    
      --overwrite                         Overwrites existing track if it shares the same trackId
    
      --skipCheck                         Skip check for whether or not the file or URL exists or if you are in a JBrowse
                                          directory
    
      --target=target                     [default: ./config.json] path to config file in JB2 installation to write out to.
    
      --trackId=trackId                   trackId for the track, by default inferred from filename, must be unique
                                          throughout config
    
    EXAMPLES
      $ jbrowse add-track /path/to/my.bam --load copy
      $ jbrowse add-track /path/to/my.bam --target /path/to/jbrowse2/installation/config.json --load symlink
      $ jbrowse add-track https://mywebsite.com/my.bam
      $ jbrowse add-track /path/to/my.bam --type AlignmentsTrack --name 'New Track' --load move
      $ jbrowse add-track /path/to/my.bam --trackId AlignmentsTrack1 --load trust --overwrite
      $ jbrowse add-track /path/to/my.bam --config '{"defaultRendering": "density"}'
    

    jbrowse add-track-json TRACK

    Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration

    USAGE
      $ jbrowse add-track-json TRACK
    
    ARGUMENTS
      TRACK  track JSON file or command line arg blob
    
    OPTIONS
      -u, --update     update the contents of an existing track, matched based on trackId
    
      --target=target  [default: ./config.json] path to config file in JB2 installation directory to write out to.
                       Creates ./config.json if nonexistent
    
    EXAMPLES
      $ jbrowse add-track-json track.json
      $ jbrowse add-track-json track.json --update
    

    jbrowse create LOCALPATH

    Downloads and installs the latest JBrowse 2 release

    USAGE
      $ jbrowse create LOCALPATH
    
    ARGUMENTS
      LOCALPATH  Location where JBrowse 2 will be installed
    
    OPTIONS
      -f, --force         Overwrites existing JBrowse 2 installation if present in path
      -h, --help          show CLI help
      -l, --listVersions  Lists out all versions of JBrowse 2
    
      -t, --tag=tag       Version of JBrowse 2 to install. Format is @gmod/jbrowse-web@0.0.1.
                          Defaults to latest
    
      -u, --url=url       A direct URL to a JBrowse 2 release
    
    EXAMPLES
      $ jbrowse create /path/to/new/installation
      $ jbrowse create /path/to/new/installation --force
      $ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip
      $ jbrowse create /path/to/new/installation --tag @gmod/jbrowse-web@0.0.1
      $ jbrowse create --listVersions # Lists out all available versions of JBrowse 2
    

    jbrowse help [COMMAND]

    display help for jbrowse

    USAGE
      $ jbrowse help [COMMAND]
    
    ARGUMENTS
      COMMAND  command to show help for
    
    OPTIONS
      --all  see all commands in CLI
    

    See code: @oclif/plugin-help

    jbrowse set-default-session

    Set a default session with views and tracks

    USAGE
      $ jbrowse set-default-session
    
    OPTIONS
      -c, --currentSession   List out the current default session
      -h, --help             show CLI help
      -n, --name=name        [default: New Default Session] Give a name for the default session
      -s, --session=session  set path to a file containing session in json format
      -t, --tracks=tracks    Track id or track ids as comma separated string to put into default session
    
      -v, --view=view        View type in config to be added as default session, i.e LinearGenomeView, CircularView,
                             DotplotView.
                             Must be provided if no default session file provided
    
      --target=target        [default: ./config.json] path to config file in JB2 installation directory to write out to
    
      --viewId=viewId        Identifier for the view. Will be generated on default
    
    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
    

    jbrowse upgrade [LOCALPATH]

    Upgrades JBrowse 2 to latest version

    USAGE
      $ jbrowse upgrade [LOCALPATH]
    
    ARGUMENTS
      LOCALPATH  [default: .] Location where JBrowse 2 is installed
    
    OPTIONS
      -h, --help          show CLI help
      -l, --listVersions  Lists out all versions of JBrowse 2
    
      -t, --tag=tag       Version of JBrowse 2 to install. Format is @gmod/jbrowse-web@0.0.1.
                          Defaults to latest
    
      -u, --url=url       A direct URL to a JBrowse 2 release
    
    EXAMPLES
      $ jbrowse upgrade # Upgrades current directory to latest jbrowse release
      $ jbrowse upgrade /path/to/jbrowse2/installation
      $ jbrowse upgrade /path/to/jbrowse2/installation --tag @gmod/jbrowse-web@0.0.1
      $ jbrowse upgrade --listVersions # Lists out all available versions of JBrowse 2
      $ jbrowse upgrade --url https://sample.com/jbrowse2.zip
    

    Debugging

    Debug logs (provded by debug) can be printed by setting the DEBUG environment variable. Setting DEBUG=* will print all debug logs. Setting DEBUG=jbrowse* will print only logs from this tool, and setting e.g. DEBUG=jbrowse:add-assembly will print only logs from the add-assembly command.

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    Install

    npm i @gmod/jbrowse-cli

    DownloadsWeekly Downloads

    2

    Version

    0.0.1-beta.23

    License

    MIT

    Unpacked Size

    133 kB

    Total Files

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