@apollo-annotation/apollo-cli

Table of contents

• Table of contents
• Usage
• Commands

Usage

$ npm install -g @apollo-annotation/apollo-cli
$ apollo COMMAND
running command...
$ apollo (--version)
@apollo-annotation/apollo-cli/0.1.10 linux-x64 node-v18.20.3
$ apollo --help [COMMAND]
USAGE
  $ apollo COMMAND
...

Commands

• apollo assembly add-fasta
• apollo assembly add-gff
• apollo assembly check
• apollo assembly delete
• apollo assembly get
• apollo assembly sequence
• apollo change get
• apollo config [KEY] [VALUE]
• apollo feature add-child
• apollo feature check
• apollo feature copy
• apollo feature delete
• apollo feature edit
• apollo feature edit-attribute
• apollo feature edit-coords
• apollo feature edit-type
• apollo feature get
• apollo feature get-id
• apollo feature import
• apollo feature search
• apollo help [COMMANDS]
• apollo login
• apollo logout
• apollo refseq get
• apollo status
• apollo user get

apollo assembly add-fasta

Add new assembly from local or external fasta file

USAGE
  $ apollo assembly add-fasta -i <value> [--profile <value>] [--config-file <value>] [-a <value>] [-x <value>] [-f]

FLAGS
  -a, --assembly=<value>     Name for this assembly. Use the file name if omitted
  -f, --force                Delete existing assembly, if it exists
  -i, --input-file=<value>   (required) Input fasta file
  -x, --index=<value>        URL of the index. Required if input is an external source and ignored if input is a local
                             file
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Add new assembly from local or external fasta file

EXAMPLES
  From local file:

    $ apollo assembly add-fasta -i genome.fa -a myAssembly

  From external source we also need the URL of the index:

    $ apollo assembly add-fasta -i https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly

See code: src/commands/assembly/add-fasta.ts

apollo assembly add-gff

Add new assembly from gff or gft file

USAGE
  $ apollo assembly add-gff -i <value> [--profile <value>] [--config-file <value>] [-a <value>] [-o] [-f]

FLAGS
  -a, --assembly=<value>     Name for this assembly. Use the file name if omitted
  -f, --force                Delete existing assembly, if it exists
  -i, --input-file=<value>   (required) Input gff or gtf file
  -o, --omit-features        Do not import features, only upload the sequences
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Add new assembly from gff or gft file

  The gff file is expected to contain sequences as per gff specifications.
  Features are also imported by default.

EXAMPLES
  Import sequences and features:

    $ apollo assembly add-gff -i genome.gff -a myAssembly

  Import sequences only:

    $ apollo assembly add-gff -i genome.gff -a myAssembly -o

See code: src/commands/assembly/add-gff.ts

apollo assembly check

Add, view, or delete checks to assembly

USAGE
  $ apollo assembly check [--profile <value>] [--config-file <value>] [-a <value>] [-c <value>] [-d]

FLAGS
  -a, --assembly=<value>     Manage checks in this assembly
  -c, --check=<value>...     Add these check names or IDs. If unset, print the checks set for assembly
  -d, --delete               Delete (instead of adding) checks
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Add, view, or delete checks to assembly

  Manage checks, i.e. the rules ensuring features in an assembly are plausible.
  This command only sets the check to apply, to retrieve features flagged by these
  checks use `apollo feature check`.

EXAMPLES
  View available check types:

    $ apollo assembly check

  View checks set for assembly hg19:

    $ apollo assembly check -a hg19

  Add checks to assembly:

    $ apollo assembly check -a hg19 -c CDSCheck

  Delete checks from assembly:

    $ apollo assembly check -a hg19 -c CDSCheck --delete

See code: src/commands/assembly/check.ts

apollo assembly delete

Delete assemblies

USAGE
  $ apollo assembly delete -a <value> [--profile <value>] [--config-file <value>] [-v]

FLAGS
  -a, --assembly=<value>...  (required) Assembly names or IDs to delete
  -v, --verbose              Print to stdout the array of assemblies deleted
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Delete assemblies

  Assemblies to delete may be names or IDs

EXAMPLES
  Delete multiple assemblies using name or ID:

    $ apollo assembly delete -a mouse 6605826fbd0eee691f83e73f

See code: src/commands/assembly/delete.ts

apollo assembly get

Get available assemblies

USAGE
  $ apollo assembly get [--profile <value>] [--config-file <value>] [-a <value>]

FLAGS
  -a, --assembly=<value>...  Get assemblies in this list of names or IDs
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Get available assemblies

  Print to stdout the list of assemblies in json format

See code: src/commands/assembly/get.ts

apollo assembly sequence

Get reference sequence in fasta format

USAGE
  $ apollo assembly sequence [--profile <value>] [--config-file <value>] [-a <value>] [-r <value>] [-s <value>] [-e
    <value>]

FLAGS
  -a, --assembly=<value>     Find input reference sequence in this assembly
  -e, --end=<value>          End coordinate
  -r, --refseq=<value>       Reference sequence. If unset, get all sequences
  -s, --start=<value>        [default: 1] Start coordinate (1-based)
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Get reference sequence in fasta format

  Return the reference sequence for a given assembly and coordinates

EXAMPLES
  Get all sequences in myAssembly:

    $ apollo assembly sequence -a myAssembly

  Get sequence in coordinates chr1:1..1000:

    $ apollo assembly sequence -a myAssembly -r chr1 -s 1 -e 1000

See code: src/commands/assembly/sequence.ts

apollo change get

Get list of changes

USAGE
  $ apollo change get [--profile <value>] [--config-file <value>] [-a <value>]

FLAGS
  -a, --assembly=<value>...  Get changes only for these assembly names or IDs (but see description)
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Get list of changes

  Return the change log in json format. Note that when an assembly is deleted the
  link between common name and ID is lost (it can still be recovered by inspecting
  the change log but at present this task is left to the user). In such cases you
  need to use the assembly ID.

See code: src/commands/change/get.ts

apollo config [KEY] [VALUE]

Get or set apollo configuration options

USAGE
  $ apollo config [KEY] [VALUE] [--profile <value>] [---file <value>] [--get-config-file]

ARGUMENTS
  KEY    Name of configuration parameter
  VALUE  Parameter value

FLAGS
  --config-file=<value>  Use this config file (mostly for testing)
  --get-config-file      Return the path to the config file and exit (this file may not exist yet)
  --profile=<value>      Profile to create or edit

DESCRIPTION
  Get or set apollo configuration options

  Use this command to create or edit a user profile with credentials to access
  Apollo. Configuration options are:

  - address:
  Address and port e.g http://localhost:3999

  - accessType:
  How to access Apollo. accessType is typically one of: google, microsoft, guest,
  root. Allowed types depend on your Apollo setup

  - accessToken:
  Access token. Usually inserted by `apollo login`

  - rootCredentials.username:
  Username of root account. Only set this for "root" access type

  - rootCredentials.password:
  Password for root account. Only set this for "root" access type

EXAMPLES
  Interactive setup:

    $ apollo config

  Setup with key/value pairs:

    $ apollo config --profile admin address http://localhost:3999

  Get current address for default profile:

    $ apollo config address

See code: src/commands/config.ts

apollo feature add-child

Add a child feature (e.g. add an exon to an mRNA)

USAGE
  $ apollo feature add-child -s <value> -e <value> -t <value> [--profile <value>] [--config-file <value>] [-i <value>]

FLAGS
  -e, --end=<value>          (required) End coordinate of the child feature (1-based)
  -i, --feature-id=<value>   [default: -] Add a child to this feature ID; use - to read it from stdin
  -s, --start=<value>        (required) Start coordinate of the child feature (1-based)
  -t, --type=<value>         (required) Type of child feature
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Add a child feature (e.g. add an exon to an mRNA)

  See the other commands under `apollo feature` to retrive the parent ID of
  interest and to populate the child feature with attributes.

EXAMPLES
  Add an exon at genomic coordinates 10..20 to this feature ID:

    $ apollo feature add-child -i 6605826fbd0eee691f83e73f -t exon -s 10 -e 20

See code: src/commands/feature/add-child.ts

apollo feature check

Get check results

USAGE
  $ apollo feature check [--profile <value>] [--config-file <value>] [-i <value>] [-a <value>]

FLAGS
  -a, --assembly=<value>       Get checks for this assembly
  -i, --feature-id=<value>...  Get checks for these feature identifiers
      --config-file=<value>    Use this config file (mostly for testing)
      --profile=<value>        Use credentials from this profile

DESCRIPTION
  Get check results

  Use this command to view which features fail checks along with the reason for
  failing. Use `apollo assembly check` for managing which checks should be applied
  to an assembly

EXAMPLES
  Get all check results in the database:

    $ apollo feature check

  Get check results for assembly hg19:

    $ apollo feature check -a hg19

See code: src/commands/feature/check.ts

apollo feature copy

Copy a feature to another location

USAGE
  $ apollo feature copy -r <value> -s <value> [--profile <value>] [--config-file <value>] [-i <value>] [-a <value>]

FLAGS
  -a, --assembly=<value>     Name or ID of target assembly. Not required if refseq is unique in the database
  -i, --feature-id=<value>   [default: -] Feature ID to copy to; use - to read it from stdin
  -r, --refseq=<value>       (required) Name or ID of target reference sequence
  -s, --start=<value>        (required) Start position in target reference sequence
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Copy a feature to another location

  The feature may be copied to the same or to a different assembly. he destination
  reference sequence may be selected by name only if unique in the database or by
  name and assembly or by identifier.

EXAMPLES
  Copy this feature ID to chr1:100 in assembly hg38:

    $ apollo feature copy -i 6605826fbd0eee691f83e73f -r chr1 -s 100 -a hg38

See code: src/commands/feature/copy.ts

apollo feature delete

Delete one or more features by ID

USAGE
  $ apollo feature delete [--profile <value>] [--config-file <value>] [-i <value>] [-f] [-n]

FLAGS
  -f, --force                  Ignore non-existing features
  -i, --feature-id=<value>...  [default: -] Feature IDs to delete
  -n, --dry-run                Only show what would be delete
      --config-file=<value>    Use this config file (mostly for testing)
      --profile=<value>        Use credentials from this profile

DESCRIPTION
  Delete one or more features by ID

  Note that deleting a child feature after deleting its parent will result in an
  error unless you set -f/--force.

See code: src/commands/feature/delete.ts

apollo feature edit

Edit features using an appropiate json input

USAGE
  $ apollo feature edit [--profile <value>] [--config-file <value>] [-j <value>]

FLAGS
  -j, --json-input=<value>   [default: -] Json string or json file or "-" to read json from stdin
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Edit features using an appropiate json input

  Edit a feature by submitting a json input with all the required attributes for
  Apollo to process it. This is a very low level command which most users probably
  do not need.

  Input may be a json string or a json file and it may be an array of changes.
  This is an example input for editing feature type:

  {
  "typeName": "TypeChange",
  "changedIds": [
  "6613f7d22c957525d631b1cc"
  ],
  "assembly": "6613f7d1360321540a11e5ed",
  "featureId": "6613f7d22c957525d631b1cc",
  "oldType": "BAC",
  "newType": "G_quartet"
  }

EXAMPLES
  Editing by passing a json to stdin:

    echo '{"typeName": ... "newType": "G_quartet"}' | apollo feature edit -j -

See code: src/commands/feature/edit.ts

apollo feature edit-attribute

Add, edit, or view a feature attribute

USAGE
  $ apollo feature edit-attribute -a <value> [--profile <value>] [--config-file <value>] [-i <value>] [-v <value>] [-d]

FLAGS
  -a, --attribute=<value>    (required) Attribute key to add or edit
  -d, --delete               Delete this attribute
  -i, --feature-id=<value>   [default: -] Feature ID to edit or "-" to read it from stdin
  -v, --value=<value>...     New attribute value. Separated mutliple values by space to them as a list. If unset return
                             current value
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Add, edit, or view a feature attribute

  Be aware that there is no checking whether attributes names and values are
  valid. For example, you can create non-unique ID attributes or you can set gene
  ontology terms to non-existing terms

EXAMPLES
  Add attribute "domains" with a list of values:

    $ apollo feature edit-attribute -i 66...3f -a domains -v ABC PLD

  Print values in "domains" as json array:

    $ apollo feature edit-attribute -i 66...3f -a domains

  Delete attribute "domains"

    $ apollo feature edit-attribute -i 66...3f -a domains -d

See code: src/commands/feature/edit-attribute.ts

apollo feature edit-coords

Edit feature start and/or end coordinates

USAGE
  $ apollo feature edit-coords [--profile <value>] [--config-file <value>] [-i <value>] [-s <value>] [-e <value>]

FLAGS
  -e, --end=<value>          New end coordinate (1-based)
  -i, --feature-id=<value>   [default: -] Feature ID to edit or "-" to read it from stdin
  -s, --start=<value>        New start coordinate (1-based)
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Edit feature start and/or end coordinates

  If editing a child feature that new coordinates must be within the parent's
  coordinates. To get the identifier of the feature to edit consider using `apollo
  feature get` or `apollo feature search`

EXAMPLES
  Edit start and end:

    $ apollo feature edit-coords -i abc...xyz -s 10 -e 1000

  Edit end and leave start as it is:

    $ apollo feature edit-coords -i abc...xyz -e 2000

See code: src/commands/feature/edit-coords.ts

apollo feature edit-type

Edit or view feature type

USAGE
  $ apollo feature edit-type [--profile <value>] [--config-file <value>] [-i <value>] [-t <value>]

FLAGS
  -i, --feature-id=<value>   [default: -] Feature ID to edit or "-" to read it from stdin
  -t, --type=<value>         Assign feature to this type. If unset return the current type
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Edit or view feature type

  Feature type is column 3 in gff format. It must be a valid sequence ontology
  term although but the valifdity of the new term is not checked.

See code: src/commands/feature/edit-type.ts

apollo feature get

Get features in assembly, reference sequence or genomic window

USAGE
  $ apollo feature get [--profile <value>] [--config-file <value>] [-a <value>] [-r <value>] [-s <value>] [-e
    <value>]

FLAGS
  -a, --assembly=<value>     Find input reference sequence in this assembly
  -e, --end=<value>          End coordinate
  -r, --refseq=<value>       Reference sequence. If unset, query all sequences
  -s, --start=<value>        [default: 1] Start coordinate (1-based)
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Get features in assembly, reference sequence or genomic window

EXAMPLES
  Get all features in myAssembly:

    $ apollo feature get -a myAssembly

  Get features intersecting chr1:1..1000. You can omit the assembly name if there
  are no other reference sequences named chr1:

    $ apollo feature get -a myAssembly -r chr1 -s 1 -e 1000

See code: src/commands/feature/get.ts

apollo feature get-id

Get features given their identifiers

USAGE
  $ apollo feature get-id [--profile <value>] [--config-file <value>] [-i <value>]

FLAGS
  -i, --feature-id=<value>...  [default: -] Retrieves feature with these IDs. Use
                               "-" to read IDs from stdin (one per
                               line)
      --config-file=<value>    Use this config file (mostly for testing)
      --profile=<value>        Use credentials from this profile

DESCRIPTION
  Get features given their identifiers

  Invalid identifiers or identifiers not found in the database will be silently
  ignored

EXAMPLES
  Get features for these identifiers:

    $ apollo feature get-id -i abc...zyz def...foo

See code: src/commands/feature/get-id.ts

apollo feature import

Import features from local gff file

USAGE
  $ apollo feature import -i <value> -a <value> [--profile <value>] [--config-file <value>] [-d]

FLAGS
  -a, --assembly=<value>     (required) Import into this assembly name or assembly ID
  -d, --delete-existing      Delete existing features before importing
  -i, --input-file=<value>   (required) Input gff or gtf file
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Import features from local gff file

  By default, features are added to the existing ones.

EXAMPLES
  Delete features in myAssembly and then import features.gff3:

    $ apollo feature import -d -i features.gff3 -a myAssembly

See code: src/commands/feature/import.ts

apollo feature search

Free text search for feature in one or more assemblies

USAGE
  $ apollo feature search -t <value> [--profile <value>] [--config-file <value>] [-a <value>]

FLAGS
  -a, --assembly=<value>...  Assembly names or IDs to search; use "-" to read it from stdin. If omitted
                             search all assemblies
  -t, --text=<value>         (required) Search for this text query
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Free text search for feature in one or more assemblies

  Return features matching a query string. This command searches only in:

  - Attribute *values* (not attribute names)
  - Source field (which in fact is stored as an attribute)
  - Feature type

  The search mode is:

  - Case insensitive
  - Match only full words, but not necessarily the full value
  - Common words are ignored. E.g. "the", "with"

  For example, given this feature:

  chr1 example SNP 10 30 0.987 . . "someKey=Fingerprint BAC with reads"

  Queries "bac" or "mRNA" return the feature. Instead these queries will NOT
  match:

  - "someKey"
  - "with"
  - "Finger"
  - "chr1"
  - "0.987"

EXAMPLES
  Search "bac" in these assemblies:

    $ apollo feature search -a mm9 mm10 -t bac

See code: src/commands/feature/search.ts

apollo help [COMMANDS]

Display help for apollo.

USAGE
  $ apollo help [COMMANDS] [-n]

ARGUMENTS
  COMMANDS  Command to show help for.

FLAGS
  -n, --nested-commands  Include all nested commands in the output.

DESCRIPTION
  Display help for apollo.

See code: @oclif/plugin-help

apollo login

Login to Apollo

USAGE
  $ apollo login [--profile <value>] [--config-file <value>] [-a <value>] [-u <value>] [-p <value>] [-f]
    [--port <value>]

FLAGS
  -a, --address=<value>      Address of Apollo server
  -f, --force                Force re-authentication even if user is already logged in
  -p, --password=<value>     Password for <username>
  -u, --username=<value>     Username for root login
      --config-file=<value>  Use this config file (mostly for testing)
      --port=<value>         [default: 3000] Get token by listening to this port number (usually this is >= 1024 and <
                             65536)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Login to Apollo

  Use the provided credentials to obtain and save the token to access Apollo. Once
  the token for the given profile has been saved in the configuration file, users
  do not normally need to execute this command again unless the token has expired.
  To setup a new profile use "apollo config"

EXAMPLES
  The most basic and probably most typical usage is to login using the default
  profile in configuration file:

    $ apollo login

  Login with a different profile:

    $ apollo login --profile my-profile

See code: src/commands/login.ts

apollo logout

Logout of Apollo

USAGE
  $ apollo logout [--profile <value>] [--config-file <value>]

FLAGS
  --config-file=<value>  Use this config file (mostly for testing)
  --profile=<value>      Use credentials from this profile

DESCRIPTION
  Logout of Apollo

  Logout by removing the access token from the selected profile

EXAMPLES
  Logout default profile:

    $ apollo logout

  Logout selected profile

    $ apollo logout --profile my-profile

See code: src/commands/logout.ts

apollo refseq get

Get reference sequences

USAGE
  $ apollo refseq get [--profile <value>] [--config-file <value>] [-a <value>]

FLAGS
  -a, --assembly=<value>...  Get reference sequences for these assembly names or IDs; use - to read it from stdin
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Get reference sequences

  Output the reference sequences in one or more assemblies in json format. This
  command returns the sequence characteristics (e.g., name, ID, etc), not the DNA
  sequences. Use `assembly sequence` for that.

EXAMPLES
  All sequences in the database:

    $ apollo refseq get

  Only sequences for these assemblies:

    $ apollo refseq get -a mm9 mm10

See code: src/commands/refseq/get.ts

apollo status

View authentication status

USAGE
  $ apollo status [--profile <value>] [--config-file <value>]

FLAGS
  --config-file=<value>  Use this config file (mostly for testing)
  --profile=<value>      Use credentials from this profile

DESCRIPTION
  View authentication status

  This command returns "<profile>: Logged in" if the selected profile has an
  access token and "<profile>: Logged out" otherwise. Note that this command does
  not check the validity of the access token.

See code: src/commands/status.ts

apollo user get

Get list of users

USAGE
  $ apollo user get [--profile <value>] [--config-file <value>] [-u <value>] [-r <value>]

FLAGS
  -r, --role=<value>         Get users with this role
  -u, --username=<value>     Find this username
      --config-file=<value>  Use this config file (mostly for testing)
      --profile=<value>      Use credentials from this profile

DESCRIPTION
  Get list of users

  If set, filters username and role must be both satisfied to return an entry

EXAMPLES
  By username:

    $ apollo user get -u Guest

  By role:

    $ apollo user get -r admin

  Use jq for more control:

    $ apollo user get | jq '.[] | select(.createdAt > "2024-03-18")'

See code: src/commands/user/get.ts