@jbrowse/cli 2.6.3 → 2.7.0

package/README.md

@@ -53,7 +53,7 @@ It is likely preferable in most cases to install the tools globally with
 - [`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 help [COMMANDS]`](#jbrowse-help-commands)
 - [`jbrowse remove-track TRACK`](#jbrowse-remove-track-track)
 - [`jbrowse set-default-session`](#jbrowse-set-default-session)
 - [`jbrowse text-index`](#jbrowse-text-index)
@@ -65,7 +65,10 @@ Add an assembly to a JBrowse 2 configuration
 
 ```
 USAGE
-  $ jbrowse add-assembly SEQUENCE
+  $ 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
@@ -76,8 +79,8 @@ ARGUMENTS
       If TYPE is bgzipFasta, the gzip index file defaults to <location>.gzi and can be
       optionally specified with --gziLocation
 
-OPTIONS
-  -a, --alias=alias
+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
 
@@ -85,16 +88,17 @@ OPTIONS
       Equivalent to `--skipCheck --overwrite`
 
   -h, --help
-      show CLI help
+      Show CLI help.
 
-  -l, --load=copy|symlink|move|inPlace
+  -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=name
+  -n, --name=<value>
       Name of the assembly; if not specified, will be guessed using the sequence file name
 
-  -t, --type=indexedFasta|bgzipFasta|twoBit|chromSizes|custom
+  -t, --type=<option>
       type of sequence, by default inferred from sequence file
 
       indexedFasta   An index FASTA (e.g. .fa or .fasta) file;
@@ -109,71 +113,97 @@ OPTIONS
 
       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=displayName
+  --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=faiLocation
+  --faiLocation=<value>
       [default: <fastaLocation>.fai] FASTA index file or URL
 
-  --gziLocation=gziLocation
+  --gziLocation=<value>
       [default: <fastaLocation>.gzi] FASTA gzip index file or URL
 
-  --out=out
+  --out=<value>
       synonym for target
 
   --overwrite
       Overwrite existing assembly if one with the same name exists
 
-  --refNameAliases=refNameAliases
+  --refNameAliases=<value>
       Reference sequence name aliases file or URL; assumed to be a tab-separated aliases
       file unless --refNameAliasesType is specified
 
-  --refNameAliasesType=aliases|custom
+  --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=refNameColors
+  --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=target
+  --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
+  # 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/v2.6.3/products/jbrowse-cli/src/commands/add-assembly.ts)_
+[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -181,53 +211,50 @@ Add a connection to a JBrowse 2 configuration
 
 ```
 USAGE
-  $ jbrowse add-connection CONNECTIONURLORPATH
+  $ 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/
 
-OPTIONS
-  -a, --assemblyNames=assemblyNames  For UCSC, optional: Comma separated list of assembly name(s) to filter from this
-                                     connection. For JBrowse: a single assembly name
-
-  -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.
+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.
+
+DESCRIPTION
+  Add a connection to a JBrowse 2 configuration
 
 EXAMPLES
   $ 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
+
+  $ 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/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.3/products/jbrowse-cli/src/commands/add-connection.ts)_
+[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.0/products/jbrowse-cli/src/commands/add-connection.ts)_
 
 ## `jbrowse add-track TRACK`
 
@@ -235,78 +262,80 @@ Add a track to a JBrowse 2 configuration
 
 ```
 USAGE
-  $ jbrowse add-track TRACK
+  $ 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
 
-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`
+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
 
-  -h, --help                            show CLI help
-
-  -l, --load=copy|symlink|move|inPlace  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
+EXAMPLES
+  # copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json
 
-  -n, --name=name                       Name of the track. Will be defaulted to the trackId if none specified
+  $ jbrowse add-track /path/to/my.bam --load copy
 
-  -t, --trackType=trackType             Type of track, by default inferred from track file
 
-  --bed1=bed1                           Used only for mcscan anchors/simpleAnchors types
 
-  --bed2=bed2                           Used only for mcscan anchors/simpleAnchors types
+  # copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json
 
-  --category=category                   Optional Comma separated string of categories to group tracks
+  $ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam
 
-  --config=config                       Any extra config settings to add to a track. i.e '{"defaultRendering":
-                                        "density"}'
 
-  --indexFile=indexFile                 Optional index file for the track
 
-  --out=out                             synonym for target
+  # same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai
 
-  --overwrite                           Overwrites existing track if it shares the same trackId
+  $ jbrowse add-track my.bam --indexFile my.bai --load copy
 
-  --protocol=protocol                   [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=subDir                       when using --load a file, output to a subdirectory of the target dir
+  # creates symlink for /path/to/my.bam and adds track to config.json
 
-  --target=target                       path to config file in JB2 installation to write out to.
+  $ jbrowse add-track /path/to/my.bam --load symlink
 
-  --trackId=trackId                     trackId for the track, by default inferred from filename, must be unique
-                                        throughout config
 
-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
+  # add track from URL to config.json, no --load flag needed
 
-  # 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
+  $ jbrowse add-track https://mywebsite.com/my.bam
 
-  # creates symlink for /path/to/my.bam and adds track to config.json
-  $ jbrowse add-track /path/to/my.bam --load symlink
 
-  # add track from URL to config.json, no --load flag needed
-  $ jbrowse add-track https://mywebsite.com/my.bam
 
   # --load inPlace adds a track without doing file operations
+
   $ jbrowse add-track /url/relative/path.bam --load inPlace
 ```
 
 _See code:
-[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.3/products/jbrowse-cli/src/commands/add-track.ts)_
+[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.0/products/jbrowse-cli/src/commands/add-track.ts)_
 
 ## `jbrowse add-track-json TRACK`
 
@@ -315,25 +344,28 @@ configuration
 
 ```
 USAGE
-  $ jbrowse add-track-json TRACK
+  $ jbrowse add-track-json TRACK [-u] [--target <value>] [--out <value>]
 
 ARGUMENTS
   TRACK  track JSON file or command line arg blob
 
-OPTIONS
-  -u, --update     update the contents of an existing track, matched based on trackId
-  --out=out        synonym for target
+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
 
-  --target=target  path to config file in JB2 installation directory to write out to.
-                   Creates ./config.json if nonexistent
+DESCRIPTION
+  Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration
 
 EXAMPLES
   $ jbrowse add-track-json track.json
+
   $ jbrowse add-track-json track.json --update
 ```
 
 _See code:
-[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.3/products/jbrowse-cli/src/commands/add-track-json.ts)_
+[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -341,30 +373,30 @@ Start up a small admin server for JBrowse configuration
 
 ```
 USAGE
-  $ jbrowse admin-server
-
-OPTIONS
-  -h, --help                     show CLI help
-
-  -p, --port=port                Specifified port to start the server on;
-                                 Default is 9090.
-
-  --bodySizeLimit=bodySizeLimit  [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=root                    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
+  $ 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 -p 8888
 ```
 
 _See code:
-[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.3/products/jbrowse-cli/src/commands/admin-server.ts)_
+[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.0/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -372,62 +404,77 @@ Downloads and installs the latest JBrowse 2 release
 
 ```
 USAGE
-  $ jbrowse create LOCALPATH
+  $ jbrowse create LOCALPATH [-h] [-f] [-l] [--branch <value>] [--nightly] [-u <value>] [-t <value>]
 
 ARGUMENTS
   LOCALPATH  Location where JBrowse 2 will be installed
 
-OPTIONS
+FLAGS
   -f, --force         Overwrites existing JBrowse 2 installation if present in path
-  -h, --help          show CLI help
+  -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 v1.0.0.
+  -t, --tag=<value>   Version of JBrowse 2 to install. Format is v1.0.0.
                       Defaults to latest
-
-  -u, --url=url       A direct URL to a JBrowse 2 release
-
-  --branch=branch     Download a development build from a named git branch
-
+  -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 create /path/to/new/installation
 
+
+
   # Download latest release from github and force overwrite existing contents at path
+
   $ jbrowse create /path/to/new/installation --force
 
+
+
   # Download latest release from a specific URL
+
   $ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip
 
+
+
   # Download a specific tag from github
+
   $ jbrowse create /path/to/new/installation --tag v1.0.0
 
+
+
   # List available versions
+
   $ jbrowse create --listVersions
 ```
 
 _See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.3/products/jbrowse-cli/src/commands/create.ts)_
+[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.0/products/jbrowse-cli/src/commands/create.ts)_
 
-## `jbrowse help [COMMAND]`
+## `jbrowse help [COMMANDS]`
 
-display help for jbrowse
+Display help for jbrowse.
 
 ```
 USAGE
-  $ jbrowse help [COMMAND]
+  $ jbrowse help [COMMANDS] [-n]
 
 ARGUMENTS
-  COMMAND  command to show help for
+  COMMANDS  Command to show help for.
+
+FLAGS
+  -n, --nested-commands  Include all nested commands in the output.
 
-OPTIONS
-  --all  see all commands in CLI
+DESCRIPTION
+  Display help for jbrowse.
 ```
 
 _See code:
-[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v3.2.14/src/commands/help.ts)_
+[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v5.2.20/src/commands/help.ts)_
 
 ## `jbrowse remove-track TRACK`
 
@@ -436,23 +483,26 @@ can cause crashes in saved sessions that refer to this track!
 
 ```
 USAGE
-  $ jbrowse remove-track TRACK
+  $ jbrowse remove-track TRACK [--target <value>] [--out <value>]
 
 ARGUMENTS
   TRACK  track JSON file or command line arg blob
 
-OPTIONS
-  --out=out        synonym for target
+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
 
-  --target=target  path to config file in JB2 installation directory to write out to.
-                   Creates ./config.json if nonexistent
+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!
 
-EXAMPLE
+EXAMPLES
   $ jbrowse remove-track-json trackId
 ```
 
 _See code:
-[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.3/products/jbrowse-cli/src/commands/remove-track.ts)_
+[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.0/products/jbrowse-cli/src/commands/remove-track.ts)_
 
 ## `jbrowse set-default-session`
 
@@ -460,37 +510,38 @@ Set a default session with views and tracks
 
 ```
 USAGE
-  $ jbrowse set-default-session
+  $ jbrowse set-default-session [-s <value>] [-n <value>] [-v <value>] [--viewId <value>] [-t <value>] [-c] [--target
+    <value>] [--out <value>] [--delete] [-h]
 
-OPTIONS
+FLAGS
   -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,
+  -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
+  -t, --tracks=<value>   Track id or track ids as comma separated string to put into default session
+  -v, --view=<value>     View type in config to be added as default session, i.e LinearGenomeView, CircularView,
                          DotplotView.
                          Must be provided if no default session file provided
-
   --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
+  --viewId=<value>       Identifier for the view. Will be generated on default
 
-  --out=out              synonym for target
-
-  --target=target        path to config file in JB2 installation directory to write out to
-
-  --viewId=viewId        Identifier for the view. Will be generated on default
+DESCRIPTION
+  Set a default session with views and tracks
 
 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 --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
 ```
 
 _See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.3/products/jbrowse-cli/src/commands/set-default-session.ts)_
+[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
 ## `jbrowse text-index`
 
@@ -498,63 +549,66 @@ Make a text-indexing file for any given track(s).
 
 ```
 USAGE
-  $ jbrowse text-index
-
-OPTIONS
-  -a, --assemblies=assemblies  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
+  $ 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).
 
-  -q, --quiet                  Hide the progress bars
+EXAMPLES
+  # indexes all tracks that it can find in the current directory's config.json
 
-  --attributes=attributes      [default: Name,ID] Comma separated list of attributes to index
+  $ jbrowse text-index
 
-  --dryrun                     Just print out tracks that will be indexed by the process, without doing any indexing
 
-  --exclude=exclude            [default: CDS,exon] Adds gene type to list of excluded types
 
-  --file=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)
+  # indexes specific trackIds that it can find in the current directory's config.json
 
-  --fileId=fileId              Set the trackId used for the indexes generated with the --file argument
+  $ jbrowse text-index --tracks=track1,track2,track3
 
-  --force                      Overwrite previously existing indexes
 
-  --out=out                    Synonym for target
 
-  --perTrack                   If set, creates an index per track
+  # indexes all tracks in a directory's config.json or in a specific config file
 
-  --prefixSize=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
+  $ jbrowse text-index --out /path/to/jb2/
 
-  --target=target              Path to config file in JB2 installation directory to read from.
 
-  --tracks=tracks              Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes
-                               all available tracks
 
-EXAMPLES
-  # indexes all tracks that it can find in the current directory's config.json
-  $ jbrowse text-index
+  # indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)
 
-  # indexes specific trackIds that it can find in the current directory's config.json
-  $ jbrowse text-index --tracks=track1,track2,track3
+  $ jbrowse text-index -a hg19 --force
 
-  # indexes all tracks in a directory's config.json or in a specific config file
-  $ jbrowse text-index --out /path/to/jb2/
 
-  # indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous
-   index already existed)
-  $ jbrowse text-index -a hg19 --force
 
   # create index for some files for use in @jbrowse/react-linear-genome-view or similar
+
   $ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes
 ```
 
 _See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.3/products/jbrowse-cli/src/commands/text-index.ts)_
+[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.0/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -562,48 +616,62 @@ Upgrades JBrowse 2 to latest version
 
 ```
 USAGE
-  $ jbrowse upgrade [LOCALPATH]
+  $ jbrowse upgrade [LOCALPATH] [-h] [-l] [-t <value>] [--branch <value>] [--nightly] [--clean] [-u <value>]
 
 ARGUMENTS
   LOCALPATH  [default: .] Location where JBrowse 2 is installed
 
-OPTIONS
-  -h, --help          show CLI help
+FLAGS
+  -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 v1.0.0.
+  -t, --tag=<value>   Version of JBrowse 2 to install. Format is v1.0.0.
                       Defaults to latest
-
-  -u, --url=url       A direct URL to a JBrowse 2 release
-
-  --branch=branch     Download a development build from a named git branch
-
+  -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
+
   $ jbrowse upgrade --url https://sample.com/jbrowse2.zip
 
+
+
   # Get nightly release from main branch
+
   $ jbrowse upgrade --nightly
 ```
 
 _See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.6.3/products/jbrowse-cli/src/commands/upgrade.ts)_
+[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.7.0/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->