@jbrowse/cli 4.0.4 → 4.1.1

package/README.md

@@ -44,428 +44,84 @@ It is likely preferable in most cases to install the tools globally with
 `npm install @jbrowse/cli -g` however
 
 ```
-
-JBrowse CLI
-
-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
-
-Use "jbrowse <command> --help" for more information about a command.
-
 ```
 
 
 ## jbrowse create
 
 ```
-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.
-                             Defaults to latest
-
-# 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
 ```
 
 
 ## jbrowse add-assembly
 
 ```
-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
-                             
-                             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
 
 ```
-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
-
-# 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
-
-# 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
 ```
 
 
 ## jbrowse text-index
 
 ```
-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
-
-# 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
-
-# indexes all tracks except specific trackIds
-$ jbrowse text-index --exclude-tracks=track1,track2,track3
-
-# 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 admin-server
 
 ```
-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)
-
-$ jbrowse admin-server
-$ jbrowse admin-server -p 8888
 ```
 
 
 ## jbrowse upgrade
 
 ```
-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
-
-# 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
 ```
 
 
 ## jbrowse make-pif
 
 ```
-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 ${file}.pif.gz.tbi
-     , --csi                     Create a CSI index for the PIF file instead of TBI
-
-$ jbrowse make-pif input.paf # creates input.pif.gz in same directory
-
-$ jbrowse make-pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also
 ```
 
 
 ## jbrowse sort-gff
 
 ```
-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 sort-gff [file] [options]
-
-Options:
-  -h, --help                    undefined
-
-# sort gff and pipe to bgzip
-$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz
-$ tabix sorted.gff.gz
-
-# sort gff from stdin
-$ cat input.gff | jbrowse sort-gff | bgzip > sorted.gff.gz
 ```
 
 
 ## jbrowse sort-bed
 
 ```
-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
-
-Usage: jbrowse sort-bed [file] [options]
-
-Options:
-  -h, --help                    undefined
-
-# sort bed and pipe to bgzip
-$ jbrowse sort-bed input.bed | bgzip > sorted.bed.gz
-$ tabix sorted.bed.gz
-
-# OR pipe data via stdin: cat file.bed | jbrowse sort-bed | bgzip > sorted.bed.gz
 ```
 
 
 ## jbrowse add-connection
 
 ```
-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
-
-$ 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-track-json
 
 ```
-Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration
-
-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
-
-$ jbrowse add-track-json track.json
-$ jbrowse add-track-json track.json --update
 ```
 
 
 ## jbrowse remove-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!
-
-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
-
-$ jbrowse remove-track trackId
 ```
 
 
 ## jbrowse set-default-session
 
 ```
-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
-
-# set default session for the config.json in your current directory
-$ jbrowse set-default-session --session /path/to/default/session.json
-
-# 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
-
-# print current default session
-$ jbrowse set-default-session --currentSession # Prints out current default session
 ```
 
 

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))