@jbrowse/cli 4.0.4 → 4.1.3

package/README.md

@@ -82,13 +82,22 @@ Downloads and installs the latest JBrowse 2 release
 Usage: jbrowse create [localPath] [options]
 
 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.
+  -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
 
 # Download latest release from github, and put in specific path
@@ -116,40 +125,79 @@ Add an assembly to a JBrowse 2 configuration
 Usage: jbrowse add-assembly <sequence> [options]
 
 Options:
-  -t, --type                    type of sequence, by default inferred from sequence file
+  -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
+                             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
+                             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
+                             twoBit - A twoBit (e.g. .2bit) file
                              
-                             chromSizes     A chromosome sizes (e.g. .chrom.sizes) 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`
+                             custom - Either a JSON file location or inline JSON
+                             that defines a custom sequence adapter; must
+                             provide --name if using inline JSON [choices:
+                             indexedFasta, bgzipFasta, twoBit, chromSizes,
+                             custom]
+
+  -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 [choices: aliases, custom]
+
+      --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 [choices: copy, symlink, move,
+                             inPlace]
+
+      --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
@@ -185,25 +233,51 @@ 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
+  -h, --help                 
+
+  -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
 
 # 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
@@ -233,21 +307,53 @@ Make a text-indexing file for any given track(s).
 Usage: jbrowse text-index [options]
 
 Options:
-  -h, --help                    Show CLI help
-     , --tracks                  Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks
-     , --excludeTracks           Specific tracks to exclude from indexing, formatted as comma separated trackIds
-     , --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
+  -h, --help                 Show CLI help
+
+      --tracks               Specific tracks to index, formatted as comma
+                             separated trackIds. If unspecified, indexes all
+                             available tracks
+
+      --excludeTracks        Specific tracks to exclude from indexing, formatted
+                             as comma separated trackIds
+
+      --target               Path to config file in JB2 installation directory
+                             to read from.
+
+      --out                  Synonym for target
+
+      --attributes           Comma separated list of attributes to index
+                             [default: Name,ID]
+
+  -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 [default:
+                             false]
+
+  -q, --quiet                Hide the progress bars [default: false]
+
+      --perTrack             If set, creates an index per track [default: false]
+
+      --exclude              Adds gene type to list of excluded types [default:
+                             CDS,exon]
+
+      --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
 
 # indexes all tracks that it can find in the current directory's config.json
 $ jbrowse text-index
@@ -277,10 +383,14 @@ Start up a small admin server for JBrowse configuration
 Usage: jbrowse admin-server [options]
 
 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)
+  -h, --help                 
+
+  -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
@@ -295,14 +405,23 @@ 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.
+  -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
+
+      --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
 
 # Upgrades current directory to latest jbrowse release
 $ jbrowse upgrade
@@ -332,9 +451,12 @@ creates pairwise indexed PAF (PIF), with bgzip and tabix
 Usage: jbrowse make-pif <file> [options]
 
 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
+  -h, --help                 
+
+      --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
 
@@ -350,7 +472,7 @@ Helper utility to sort GFF files for tabix. Moves all lines starting with # to t
 Usage: jbrowse sort-gff [file] [options]
 
 Options:
-  -h, --help                    undefined
+  -h, --help                 
 
 # sort gff and pipe to bgzip
 $ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz
@@ -369,7 +491,7 @@ Helper utility to sort BED files for tabix. Moves all lines starting with # to t
 Usage: jbrowse sort-bed [file] [options]
 
 Options:
-  -h, --help                    undefined
+  -h, --help                 
 
 # sort bed and pipe to bgzip
 $ jbrowse sort-bed input.bed | bgzip > sorted.bed.gz
@@ -387,17 +509,35 @@ Add a connection to a JBrowse 2 configuration
 Usage: jbrowse add-connection <connectionUrlOrPath> [options]
 
 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
+  -h, --help                 
+
+  -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
 
 $ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19
 $ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38
@@ -416,10 +556,15 @@ Add a track configuration directly from a JSON hunk to the JBrowse 2 configurati
 Usage: jbrowse add-track-json <track> [options]
 
 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
+  -h, --help                 
+
+  -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 add-track-json track.json
 $ jbrowse add-track-json track.json --update
@@ -434,9 +579,12 @@ Remove a track configuration from a JBrowse 2 configuration. Be aware that this
 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
+  -h, --help                 
+
+      --target               Path to config file in JB2 installation directory
+                             to write out to
+
+      --out                  Synonym for target
 
 $ jbrowse remove-track trackId
 ```
@@ -450,13 +598,23 @@ Set a default session with views and tracks
 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
+  -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 [default: New
+                             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

package/bin/run

@@ -1,3 +1,4 @@
 #!/usr/bin/env node
 
-require('../dist/index.js').main(process.argv.slice(2))
+import { main } from '../dist/index.js'
+main(process.argv.slice(2))