@jbrowse/cli 3.5.1 → 3.6.0

package/README.md

@@ -43,741 +43,425 @@ 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 make-pif FILE`](#jbrowse-make-pif-file)
-- [`jbrowse remove-track TRACK`](#jbrowse-remove-track-track)
-- [`jbrowse set-default-session`](#jbrowse-set-default-session)
-- [`jbrowse sort-bed FILE`](#jbrowse-sort-bed-file)
-- [`jbrowse sort-gff FILE`](#jbrowse-sort-gff-file)
-- [`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 [-t indexedFasta|bgzipFasta|twoBit|chromSizes|custom] [-n <value>] [-a
-    <value>...] [--displayName <value>] [--faiLocation <value>] [--gziLocation <value>] [--refNameAliasesType
-    aliases|custom --refNameAliases <value>] [--refNameColors <value>] [--target <value>] [--out <value>] [-h] [-l
-    copy|symlink|move|inPlace] [--skipCheck] [--overwrite] [-f]
-
-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
-
-FLAGS
-  -a, --alias=<value>...
-      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=<option>
-      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>
-
-  -n, --name=<value>
-      Name of the assembly; if not specified, will be guessed using the sequence file name
-
-  -t, --type=<option>
-      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
-      <options: indexedFasta|bgzipFasta|twoBit|chromSizes|custom>
-
-  --displayName=<value>
-      The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier
-      like "hg38"
-
-  --faiLocation=<value>
-      [default: <fastaLocation>.fai] FASTA index file or URL
-
-  --gziLocation=<value>
-      [default: <fastaLocation>.gzi] FASTA gzip index file or URL
-
-  --out=<value>
-      synonym for target
-
-  --overwrite
-      Overwrite existing assembly if one with the same name exists
-
-  --refNameAliases=<value>
-      Reference sequence name aliases file or URL; assumed to be a tab-separated aliases
-      file unless --refNameAliasesType is specified
-
-  --refNameAliasesType=<option>
-      Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either
-      a JSON file location or inline JSON that defines a custom sequence adapter
-      <options: aliases|custom>
-
-  --refNameColors=<value>
-      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=<value>
-      path to config file in JB2 installation directory to write out to.
-      Creates ./config.json if nonexistent
-
-DESCRIPTION
-  Add an assembly to a JBrowse 2 configuration
-
-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 CLI
 
-  $ 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
+USAGE
+  $ jbrowse <command> [options]
 
+COMMANDS
+  create               Downloads and installs the latest JBrowse 2 release
+  add-assembly         Add an assembly to a JBrowse 2 configuration
+  add-track            Add a track to a JBrowse 2 configuration
+  text-index           Make a text-indexing file for any given track(s)
+  admin-server         Start up a small admin server for JBrowse configuration
+  upgrade              Upgrades JBrowse 2 to latest version
+  make-pif             Creates pairwise indexed PAF (PIF), with bgzip and tabix
+  sort-gff             Helper utility to sort GFF files for tabix
+  sort-bed             Helper utility to sort BED files for tabix
+  add-connection       Add a connection to a JBrowse 2 configuration
+  add-track-json       Add a track configuration directly from a JSON hunk
+  remove-track         Remove a track configuration from a JBrowse 2 configuration
+  set-default-session  Set a default session with views and tracks
 
+OPTIONS
+  -h, --help     Show help
+  -v, --version  Show version
 
-  # add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists
+Use "jbrowse <command> --help" for more information about a command.
 
-  $ jbrowse add-assembly myfile.fa.gz --load copy
 ```
 
-_See code:
-[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v3.5.1/products/jbrowse-cli/src/commands/add-assembly.ts)_
-
-## `jbrowse add-connection CONNECTIONURLORPATH`
 
-Add a connection to a JBrowse 2 configuration
+## jbrowse create
 
 ```
-USAGE
-  $ jbrowse add-connection CONNECTIONURLORPATH [-t <value>] [-a <value>] [-c <value>] [--connectionId <value>] [-n
-    <value>] [--target <value>] [--out <value>] [-h] [--skipCheck] [--overwrite] [-f]
-
-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/
-
-FLAGS
-  -a, --assemblyNames=<value>  For UCSC, optional: Comma separated list of assembly name(s) to filter from this
-                               connection. For JBrowse: a single assembly name
-  -c, --config=<value>         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=<value>           Name of the connection. Defaults to connectionId if not provided
-  -t, --type=<value>           type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom
-      --connectionId=<value>   Id for the connection that must be unique to JBrowse.  Defaults to
-                               'connectionType-assemblyName-currentTime'
-      --out=<value>            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=<value>         path to config file in JB2 installation directory to write out to.
+Downloads and installs the latest JBrowse 2 release
 
-DESCRIPTION
-  Add a connection to a JBrowse 2 configuration
+Usage: jbrowse create [localPath] [options]
 
-EXAMPLES
-  $ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19
+Options:
+  -h, --help                    Show help
+  -f, --force                   Overwrites existing JBrowse 2 installation if present in path
+  -l, --listVersions            Lists out all versions of JBrowse 2
+     , --branch                  Download a development build from a named git branch
+     , --nightly                 Download the latest development build from the main branch
+  -u, --url                     A direct URL to a JBrowse 2 release
+  -t, --tag                     Version of JBrowse 2 to install. Format is v1.0.0.
+                             Defaults to latest
 
-  $ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38
+# Download latest release from github, and put in specific path
+$ jbrowse create /path/to/new/installation
 
-  $ jbrowse add-connection http://mysite.com/path/to/hub.txt
+# Download latest release from github and force overwrite existing contents at path
+$ jbrowse create /path/to/new/installation --force
 
-  $ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection
+# Download latest release from a specific URL
+$ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip
 
-  $ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19
+# Download a specific tag from github
+$ jbrowse create /path/to/new/installation --tag v1.0.0
 
-  $ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json
+# List available versions
+$ jbrowse create --listVersions
 ```
 
-_See code:
-[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v3.5.1/products/jbrowse-cli/src/commands/add-connection.ts)_
-
-## `jbrowse add-track TRACK`
 
-Add a track to a JBrowse 2 configuration
+## jbrowse add-assembly
 
 ```
-USAGE
-  $ jbrowse add-track TRACK [-t <value>] [-n <value>] [--indexFile <value>] [-d <value>] [-a <value>]
-    [--category <value>] [--config <value>] [--target <value>] [--out <value>] [--subDir <value>] [-h] [--trackId
-    <value>] [-l copy|symlink|move|inPlace] [--skipCheck] [--overwrite] [-f] [--protocol <value>] [--bed1 <value>]
-    [--bed2 <value>]
-
-ARGUMENTS
-  TRACK  Track file or URL
-
-FLAGS
-  -a, --assemblyNames=<value>  Assembly name or names for track as comma separated string. If none, will default to the
-                               assembly in your config file
-  -d, --description=<value>    Optional description of the track
-  -f, --force                  Equivalent to `--skipCheck --overwrite`
-  -h, --help                   Show CLI help.
-  -l, --load=<option>          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>
-  -n, --name=<value>           Name of the track. Will be defaulted to the trackId if none specified
-  -t, --trackType=<value>      Type of track, by default inferred from track file
-      --bed1=<value>           Used only for mcscan anchors/simpleAnchors types
-      --bed2=<value>           Used only for mcscan anchors/simpleAnchors types
-      --category=<value>       Optional Comma separated string of categories to group tracks
-      --config=<value>         Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'
-      --indexFile=<value>      Optional index file for the track
-      --out=<value>            synonym for target
-      --overwrite              Overwrites existing track if it shares the same trackId
-      --protocol=<value>       [default: uri] Force protocol to a specific value
-      --skipCheck              Skip check for whether or not the file or URL exists or if you are in a JBrowse directory
-      --subDir=<value>         when using --load a file, output to a subdirectory of the target dir
-      --target=<value>         path to config file in JB2 installation to write out to.
-      --trackId=<value>        trackId for the track, by default inferred from filename, must be unique throughout
-                               config
-
-DESCRIPTION
-  Add a track to a JBrowse 2 configuration
-
-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
-
-
+Add an assembly to a JBrowse 2 configuration
 
-  # creates symlink for /path/to/my.bam and adds track to config.json
+Usage: jbrowse add-assembly <sequence> [options]
+
+Options:
+  -t, --type                    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
+  -n, --name                    Name of the assembly; if not specified, will be guessed using the sequence file name
+  -a, --alias                   An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38");
+                             can be specified multiple times
+     , --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             [default: <fastaLocation>.fai] FASTA index file or URL
+     , --gziLocation             [default: <fastaLocation>.gzi] FASTA gzip index file or URL
+     , --refNameAliases          Reference sequence name aliases file or URL; assumed to be a tab-separated aliases
+                             file unless --refNameAliasesType is specified
+     , --refNameAliasesType      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           A comma-separated list of color strings for the reference sequence names; will cycle
+                             through colors if there are fewer colors than sequences
+     , --target                  path to config file in JB2 installation directory to write out to.
+                             Creates ./config.json if nonexistent
+     , --out                     synonym for target
+  -h, --help                    Display help for command
+  -l, --load                    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
+     , --skipCheck               Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory
+     , --overwrite               Overwrite existing assembly if one with the same name exists
+  -f, --force                   Equivalent to `--skipCheck --overwrite`
+
+# 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
+```
+
+
+## jbrowse add-track
 
-  $ jbrowse add-track /path/to/my.bam --load symlink
+```
+Add a track to a JBrowse 2 configuration
 
+Usage: jbrowse add-track <track> [options]
 
+Options:
+  -h, --help                    undefined
+  -t, --trackType               Type of track, by default inferred from track file
+  -n, --name                    Name of the track. Will be defaulted to the trackId if none specified
+     , --indexFile               Optional index file for the track
+  -d, --description             Optional description of the track
+  -a, --assemblyNames           Assembly name or names for track as comma separated string
+     , --category                Optional comma separated string of categories to group tracks
+     , --config                  Any extra config settings to add to a track
+     , --target                  Path to config file in JB2 installation to write out to
+     , --out                     Synonym for target
+     , --subDir                  When using --load a file, output to a subdirectory of the target dir
+     , --trackId                 trackId for the track, by default inferred from filename
+  -l, --load                    How to manage the track (copy, symlink, move, inPlace)
+     , --skipCheck               Skip check for whether file or URL exists
+     , --overwrite               Overwrites existing track if it shares the same trackId
+  -f, --force                   Equivalent to --skipCheck --overwrite
+     , --protocol                Force protocol to a specific value
+     , --bed1                    Used only for mcscan anchors/simpleAnchors types
+     , --bed2                    Used only for mcscan anchors/simpleAnchors types
 
-  # add track from URL to config.json, no --load flag needed
+# 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
 
-  $ jbrowse add-track https://mywebsite.com/my.bam
+# 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
 
-  # --load inPlace adds a track without doing file operations
+# add track from URL to config.json, no --load flag needed
+$ jbrowse add-track https://mywebsite.com/my.bam
 
-  $ jbrowse add-track /url/relative/path.bam --load inPlace
+# --load inPlace adds a track without doing file operations
+$ jbrowse add-track /url/relative/path.bam --load inPlace
 ```
 
-_See code:
-[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v3.5.1/products/jbrowse-cli/src/commands/add-track.ts)_
-
-## `jbrowse add-track-json TRACK`
 
-Add a track configuration directly from a JSON hunk to the JBrowse 2
-configuration
+## jbrowse text-index
 
 ```
-USAGE
-  $ jbrowse add-track-json TRACK [-u] [--target <value>] [--out <value>]
-
-ARGUMENTS
-  TRACK  track JSON file or command line arg blob
-
-FLAGS
-  -u, --update          update the contents of an existing track, matched based on trackId
-      --out=<value>     synonym for target
-      --target=<value>  path to config file in JB2 installation directory to write out to.
-                        Creates ./config.json if nonexistent
+Make a text-indexing file for any given track(s).
 
-DESCRIPTION
-  Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration
+Usage: jbrowse text-index [options]
 
-EXAMPLES
-  $ jbrowse add-track-json track.json
+Options:
+  -h, --help                    Show CLI help
+     , --tracks                  Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks
+     , --target                  Path to config file in JB2 installation directory to read from.
+     , --out                     Synonym for target
+     , --attributes              Comma separated list of attributes to index
+  -a, --assemblies              Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config
+     , --force                   Overwrite previously existing indexes
+  -q, --quiet                   Hide the progress bars
+     , --perTrack                If set, creates an index per track
+     , --exclude                 Adds gene type to list of excluded types
+     , --prefixSize              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
+     , --file                    File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)
+     , --fileId                  Set the trackId used for the indexes generated with the --file argument
+     , --dryrun                  Just print out tracks that will be indexed by the process, without doing any indexing
 
-  $ jbrowse add-track-json track.json --update
-```
+# indexes all tracks that it can find in the current directory's config.json
+$ jbrowse text-index
 
-_See code:
-[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v3.5.1/products/jbrowse-cli/src/commands/add-track-json.ts)_
+# indexes specific trackIds that it can find in the current directory's config.json
+$ jbrowse text-index --tracks=track1,track2,track3
 
-## `jbrowse admin-server`
+# indexes all tracks in a directory's config.json or in a specific config file
+$ jbrowse text-index --out /path/to/jb2/
 
-Start up a small admin server for JBrowse configuration
+# 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-view2 or similar
+$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes
 ```
-USAGE
-  $ jbrowse admin-server [-p <value>] [--root <value>] [--bodySizeLimit <value>] [-h]
-
-FLAGS
-  -h, --help                   Show CLI help.
-  -p, --port=<value>           Specifified port to start the server on;
-                               Default is 9090.
-      --bodySizeLimit=<value>  [default: 25mb] Size limit of the update message; may need to increase if config is
-                               large.
-                               Argument is passed to bytes library for parsing: https://www.npmjs.com/package/bytes.
-      --root=<value>           path to the root of the JB2 installation.
-                               Creates ./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
 
-DESCRIPTION
-  Start up a small admin server for JBrowse configuration
 
-EXAMPLES
-  $ jbrowse admin-server
+## jbrowse admin-server
 
-  $ jbrowse admin-server -p 8888
 ```
+Start up a small admin server for JBrowse configuration
 
-_See code:
-[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v3.5.1/products/jbrowse-cli/src/commands/admin-server.ts)_
-
-## `jbrowse create LOCALPATH`
+Usage: jbrowse admin-server [options]
 
-Downloads and installs the latest JBrowse 2 release
+Options:
+  -h, --help                    undefined
+  -p, --port                    Specified port to start the server on (default: 9090)
+     , --root                    Path to the root of the JB2 installation
+     , --bodySizeLimit           Size limit of the update message (default: 25mb)
 
+$ jbrowse admin-server
+$ jbrowse admin-server -p 8888
 ```
-USAGE
-  $ jbrowse create LOCALPATH [-h] [-f] [-l] [--branch <value>] [--nightly] [-u <value>] [-t <value>]
-
-ARGUMENTS
-  LOCALPATH  Location where JBrowse 2 will be installed
-
-FLAGS
-  -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=<value>     Version of JBrowse 2 to install. Format is v1.0.0.
-                        Defaults to latest
-  -u, --url=<value>     A direct URL to a JBrowse 2 release
-      --branch=<value>  Download a development build from a named git branch
-      --nightly         Download the latest development build from the main branch
 
-DESCRIPTION
-  Downloads and installs the latest JBrowse 2 release
 
-EXAMPLES
-  # Download latest release from github, and put in specific path
+## jbrowse upgrade
 
-  $ 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
+```
+Upgrades JBrowse 2 to latest version
 
+Usage: jbrowse upgrade [localPath] [options]
 
+Options:
+  -h, --help                    Display help for command
+  -l, --listVersions            Lists out all versions of JBrowse 2
+  -t, --tag                     Version of JBrowse 2 to install. Format is v1.0.0.
+                             Defaults to latest
+     , --branch                  Download a development build from a named git branch
+     , --nightly                 Download the latest development build from the main branch
+     , --clean                   Removes old js,map,and LICENSE files in the installation
+  -u, --url                     A direct URL to a JBrowse 2 release
 
-  # List available versions
+# Upgrades current directory to latest jbrowse release
+$ jbrowse upgrade
 
-  $ jbrowse create --listVersions
-```
+# Upgrade jbrowse instance at a specific filesystem path
+$ jbrowse upgrade /path/to/jbrowse2/installation
 
-_See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v3.5.1/products/jbrowse-cli/src/commands/create.ts)_
+# Upgrade to a specific tag
+$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0
 
-## `jbrowse help [COMMAND]`
+# List versions available on github
+$ jbrowse upgrade --listVersions
 
-Display help for jbrowse.
+# Upgrade from a specific URL
+$ jbrowse upgrade --url https://sample.com/jbrowse2.zip
 
+# Get nightly release from main branch
+$ jbrowse upgrade --nightly
 ```
-USAGE
-  $ jbrowse help [COMMAND...] [-n]
 
-ARGUMENTS
-  COMMAND...  Command to show help for.
 
-FLAGS
-  -n, --nested-commands  Include all nested commands in the output.
+## jbrowse make-pif
 
-DESCRIPTION
-  Display help for jbrowse.
 ```
-
-_See code:
-[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.2.28/src/commands/help.ts)_
-
-## `jbrowse make-pif FILE`
-
 creates pairwise indexed PAF (PIF), with bgzip and tabix
 
-```
-USAGE
-  $ jbrowse make-pif FILE [--out <value>] [--csi] [-h]
-
-ARGUMENTS
-  FILE  PAF file as input
-
-FLAGS
-  -h, --help         Show CLI help.
-      --csi          Create a CSI index for the PIF file instead of TBI
-      --out=<value>  Where to write the output file. will write ${file}.pif.gz and ${file}.pif.gz.tbi
-
-DESCRIPTION
-  creates pairwise indexed PAF (PIF), with bgzip and tabix
+Usage: jbrowse make-pif <file> [options]
 
-EXAMPLES
-  $ jbrowse pif input.paf # creates input.pif.gz in same directory
+Options:
+  -h, --help                    undefined
+     , --out                     Where to write the output file. will write ${file}.pif.gz and ${file}.pif.gz.tbi
+     , --csi                     Create a CSI index for the PIF file instead of TBI
 
+$ jbrowse make-pif input.paf # creates input.pif.gz in same directory
 
-
-  $ jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also
+$ jbrowse make-pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also
 ```
 
-_See code:
-[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v3.5.1/products/jbrowse-cli/src/commands/make-pif.ts)_
-
-## `jbrowse remove-track TRACK`
 
-Remove a track configuration from a JBrowse 2 configuration. Be aware that this
-can cause crashes in saved sessions that refer to this track!
+## jbrowse sort-gff
 
 ```
-USAGE
-  $ jbrowse remove-track TRACK [--target <value>] [--out <value>]
+Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep
 
-ARGUMENTS
-  TRACK  track JSON file or command line arg blob
+Usage: jbrowse sort-gff [file] [options]
 
-FLAGS
-  --out=<value>     synonym for target
-  --target=<value>  path to config file in JB2 installation directory to write out to.
-                    Creates ./config.json if nonexistent
+Options:
+  -h, --help                    undefined
 
-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!
+# sort gff and pipe to bgzip
+$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz
+$ tabix sorted.gff.gz
 
-EXAMPLES
-  $ jbrowse remove-track-json trackId
+# sort gff from stdin
+$ cat input.gff | jbrowse sort-gff | bgzip > sorted.gff.gz
 ```
 
-_See code:
-[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v3.5.1/products/jbrowse-cli/src/commands/remove-track.ts)_
 
-## `jbrowse set-default-session`
-
-Set a default session with views and tracks
+## jbrowse sort-bed
 
 ```
-USAGE
-  $ jbrowse set-default-session [-s <value>] [-n <value>] [-c] [--target <value>] [--out <value>] [--delete] [-h]
-
-FLAGS
-  -c, --currentSession   List out the current default session
-  -h, --help             Show CLI help.
-  -n, --name=<value>     [default: New Default Session] Give a name for the default session
-  -s, --session=<value>  set path to a file containing session in json format (required, unless using
-                         delete/currentSession flags)
-      --delete           Delete any existing default session.
-      --out=<value>      synonym for target
-      --target=<value>   path to config file in JB2 installation directory to write out to
-
-DESCRIPTION
-  Set a default session with views and tracks
-
-EXAMPLES
-  # set default session for the config.json in your current directory
-
-  $ jbrowse set-default-session --session /path/to/default/session.json
-
-
+Helper utility to sort BED files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep
 
-  # make session.json the defaultSession on the specified target config.json file
+Usage: jbrowse sort-bed [file] [options]
 
-  $ jbrowse set-default-session --target /path/to/jb2/installation/config.json --session session.json
+Options:
+  -h, --help                    undefined
 
+# sort bed and pipe to bgzip
+$ jbrowse sort-bed input.bed | bgzip > sorted.bed.gz
+$ tabix sorted.bed.gz
 
-
-  # print current default session
-
-  $ jbrowse set-default-session --currentSession # Prints out current default session
+# OR pipe data via stdin: cat file.bed | jbrowse sort-bed | bgzip > sorted.bed.gz
 ```
 
-_See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v3.5.1/products/jbrowse-cli/src/commands/set-default-session.ts)_
-
-## `jbrowse sort-bed FILE`
 
-Helper utility to sort GFF files for tabix. Moves all lines starting with # to
-the top of the file, and sort by refname and start position using unix utilities
-sort and grep
+## jbrowse add-connection
 
 ```
-USAGE
-  $ jbrowse sort-bed FILE [-h]
-
-ARGUMENTS
-  FILE  GFF file
-
-FLAGS
-  -h, --help  Show CLI help.
-
-DESCRIPTION
-  Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by
-  refname and start position using unix utilities sort and grep
+Add a connection to a JBrowse 2 configuration
 
-EXAMPLES
-  # sort gff and pipe to bgzip
+Usage: jbrowse add-connection <connectionUrlOrPath> [options]
 
-  $ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz
+Options:
+  -h, --help                    undefined
+  -t, --type                    Type of connection (e.g. JBrowse1Connection, UCSCTrackHubConnection, custom)
+  -a, --assemblyNames           For UCSC: optional comma separated list of assembly names to filter. For JBrowse1: a single assembly name
+  -c, --config                  Extra config settings to add to connection in JSON object format
+     , --connectionId            Id for the connection that must be unique to JBrowse
+  -n, --name                    Name of the connection. Defaults to connectionId if not provided
+     , --target                  Path to config file in JB2 installation directory to write out to
+     , --out                     Synonym for target
+     , --skipCheck               Don't check whether the data directory URL exists
+     , --overwrite               Overwrites any existing connections if same connection id
+  -f, --force                   Equivalent to --skipCheck --overwrite
 
-  $ tabix sorted.gff.gz
+$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19
+$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38
+$ jbrowse add-connection http://mysite.com/path/to/hub.txt
+$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection
+$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19
+$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json
 ```
 
-_See code:
-[src/commands/sort-bed.ts](https://github.com/GMOD/jbrowse-components/blob/v3.5.1/products/jbrowse-cli/src/commands/sort-bed.ts)_
-
-## `jbrowse sort-gff FILE`
 
-Helper utility to sort GFF files for tabix. Moves all lines starting with # to
-the top of the file, and sort by refname and start position using unix utilities
-sort and grep
+## jbrowse add-track-json
 
 ```
-USAGE
-  $ jbrowse sort-gff FILE [-h]
-
-ARGUMENTS
-  FILE  GFF file
-
-FLAGS
-  -h, --help  Show CLI help.
+Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration
 
-DESCRIPTION
-  Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by
-  refname and start position using unix utilities sort and grep
+Usage: jbrowse add-track-json <track> [options]
 
-EXAMPLES
-  # sort gff and pipe to bgzip
+Options:
+  -h, --help                    undefined
+  -u, --update                  Update the contents of an existing track, matched based on trackId
+     , --target                  Path to config file in JB2 installation directory to write out to
+     , --out                     Synonym for target
 
-  $ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz
-
-  $ tabix sorted.gff.gz
+$ jbrowse add-track-json track.json
+$ jbrowse add-track-json track.json --update
 ```
 
-_See code:
-[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v3.5.1/products/jbrowse-cli/src/commands/sort-gff.ts)_
-
-## `jbrowse text-index`
 
-Make a text-indexing file for any given track(s).
+## jbrowse remove-track
 
 ```
-USAGE
-  $ jbrowse text-index [-h] [--tracks <value>] [--target <value>] [--out <value>] [--attributes <value>] [-a
-    <value>] [--force] [-q] [--perTrack] [--exclude <value>] [--prefixSize <value>] [--file <value>...] [--fileId
-    <value>...] [--dryrun]
-
-FLAGS
-  -a, --assemblies=<value>  Specify the assembl(ies) to create an index for. If unspecified, creates an index for each
-                            assembly in the config
-  -h, --help                Show CLI help.
-  -q, --quiet               Hide the progress bars
-      --attributes=<value>  [default: Name,ID] Comma separated list of attributes to index
-      --dryrun              Just print out tracks that will be indexed by the process, without doing any indexing
-      --exclude=<value>     [default: CDS,exon] Adds gene type to list of excluded types
-      --file=<value>...     File or files to index (can be used to create trix indexes for embedded component use cases
-                            not using a config.json for example)
-      --fileId=<value>...   Set the trackId used for the indexes generated with the --file argument
-      --force               Overwrite previously existing indexes
-      --out=<value>         Synonym for target
-      --perTrack            If set, creates an index per track
-      --prefixSize=<value>  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
-      --target=<value>      Path to config file in JB2 installation directory to read from.
-      --tracks=<value>      Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all
-                            available tracks
-
-DESCRIPTION
-  Make a text-indexing file for any given track(s).
-
-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
+Remove a track configuration from a JBrowse 2 configuration. Be aware that this can cause crashes in saved sessions that refer to this track!
 
+Usage: jbrowse remove-track <trackId> [options]
 
+Options:
+  -h, --help                    undefined
+     , --target                  Path to config file in JB2 installation directory to write out to
+     , --out                     Synonym for target
 
-  # 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-view2 or similar
-
-  $ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes
+$ jbrowse remove-track trackId
 ```
 
-_See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v3.5.1/products/jbrowse-cli/src/commands/text-index.ts)_
 
-## `jbrowse upgrade [LOCALPATH]`
-
-Upgrades JBrowse 2 to latest version
+## jbrowse set-default-session
 
 ```
-USAGE
-  $ jbrowse upgrade [LOCALPATH] [-h] [-l] [-t <value>] [--branch <value>] [--nightly] [--clean] [-u <value>]
-
-ARGUMENTS
-  LOCALPATH  [default: .] Location where JBrowse 2 is installed
-
-FLAGS
-  -h, --help            Show CLI help.
-  -l, --listVersions    Lists out all versions of JBrowse 2
-  -t, --tag=<value>     Version of JBrowse 2 to install. Format is v1.0.0.
-                        Defaults to latest
-  -u, --url=<value>     A direct URL to a JBrowse 2 release
-      --branch=<value>  Download a development build from a named git branch
-      --clean           Removes old js,map,and LICENSE files in the installation
-      --nightly         Download the latest development build from the main branch
-
-DESCRIPTION
-  Upgrades JBrowse 2 to latest version
-
-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
+Set a default session with views and tracks
 
-  $ jbrowse upgrade --url https://sample.com/jbrowse2.zip
+Usage: jbrowse add-track <track> [options]
 
+Options:
+  -s, --session                 set path to a file containing session in json format (required, unless using delete/currentSession flags)
+  -n, --name                    Give a name for the default session
+  -c, --currentSession          List out the current default session
+     , --target                  path to config file in JB2 installation directory to write out to
+     , --out                     synonym for target
+     , --delete                  Delete any existing default session.
+  -h, --help                    Show help
 
+# set default session for the config.json in your current directory
+$ jbrowse set-default-session --session /path/to/default/session.json
 
-  # Get nightly release from main branch
+# make session.json the defaultSession on the specified target config.json file
+$ jbrowse set-default-session --target /path/to/jb2/installation/config.json --session session.json
 
-  $ jbrowse upgrade --nightly
+# print current default session
+$ jbrowse set-default-session --currentSession # Prints out current default session
 ```
 
-_See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v3.5.1/products/jbrowse-cli/src/commands/upgrade.ts)_
-
-<!-- commandsstop -->
-
-## Debugging
 
-Debug logs (provided by [debug](https://github.com/visionmedia/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.