$ npm install -g @apollo-annotation/cli
$ apollo COMMAND
running command...
$ apollo (--version)
@apollo-annotation/cli/1.1.0 linux-x64 node-v24.14.1
$ apollo --help [COMMAND]
USAGE
$ apollo COMMAND
...apollo assembly add-from-fasta INPUTapollo assembly add-from-gff INPUT-FILEapollo assembly checkapollo assembly deleteapollo assembly getapollo assembly sequenceapollo change getapollo config [KEY] [VALUE]apollo export gff3 ASSEMBLYapollo feature add [FEATURE-JSON]apollo feature add-childapollo feature checkapollo feature copyapollo feature deleteapollo feature editapollo feature edit-attributeapollo feature edit-coordsapollo feature edit-typeapollo feature getapollo feature get-idapollo feature get-indexed-id IDapollo feature import INPUT-FILEapollo feature searchapollo file deleteapollo file downloadapollo file getapollo file upload INPUT-FILEapollo help [COMMANDS]apollo jbrowse desktop JBROWSEFILEapollo jbrowse get-configapollo jbrowse set-config INPUTFILEapollo loginapollo logoutapollo refseq add-alias INPUT-FILEapollo refseq getapollo statusapollo user get
Add a new assembly from fasta input
USAGE
$ apollo assembly add-from-fasta INPUT [--profile <value>] [--config-file <value>] [-a <value>] [-f] [-e] [--fai <value>]
[--gzi <value>] [-z | -d]
ARGUMENTS
INPUT Input fasta file, local or remote, or id of a previously uploaded file. For local or remote files, it is
assumed the file is bgzip'd with `bgzip` and indexed with `samtools faidx`. The indexes are assumed to be at
<my.fasta.gz>.fai and <my.fasta.gz>.gzi unless the options --fai and --gzi are provided. A local file can be
uncompressed if the flag -e/--editable is set (but see below about using -e)
FLAGS
-a, --assembly=<value> Name for this assembly. Use the file name if omitted
-d, --decompressed For local file input: Override autodetection and instruct that input is decompressed
-e, --editable Instead of using indexed fasta lookup, the sequence is loaded into the Apollo database and
is editable. Use with caution, as editing the sequence often has unintended side effects.
-f, --force Delete existing assembly, if it exists
-z, --gzip For local file input: Override autodetection and instruct that input is gzip compressed
--config-file=<value> Use this config file (mostly for testing)
--fai=<value> Fasta index of the (not-editable) fasta file
--gzi=<value> Gzi index of the (not-editable) fasta file
--profile=<value> Use credentials from this profile
DESCRIPTION
Add a new assembly from fasta input
Add new assembly. The input fasta may be:
* A local file bgzip'd and indexed. It can be uncompressed if the -e/--editable is set (but see description of -e)
* An external fasta file bgzip'd and indexed
* The id of a file previously uploaded to Apollo
EXAMPLES
From local file assuming indexes genome.gz.fai and genome.gz.gzi are present:
$ apollo assembly add-from-fasta genome.fa.gz -a myAssembly
Local file with editable sequence does not require compression and indexing:
$ apollo assembly add-from-fasta genome.fa -a myAssembly
From external source assuming there are also indexes https://.../genome.fa.gz.fai and https://.../genome.fa.gz.gzi:
$ apollo assembly add-from-fasta https://.../genome.fa.gz -a myAssembly
See code: src/commands/assembly/add-from-fasta.ts
Add new assembly from gff or gft file
USAGE
$ apollo assembly add-from-gff INPUT-FILE [--profile <value>] [--config-file <value>] [-a <value>] [-o] [-f]
[--no-strict]
ARGUMENTS
INPUT-FILE Input gff file
FLAGS
-a, --assembly=<value> Name for this assembly. Use the file name if omitted
-f, --force Delete existing assembly, if it exists
-o, --omit-features Do not import features, only upload the sequences
--config-file=<value> Use this config file (mostly for testing)
--no-strict If any feature lines in the GFF3 can't be processed, skip them instead of aborting the
import
--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-from-gff genome.gff -a myAssembly
Import sequences only:
$ apollo assembly add-from-gff genome.gff -a myAssembly -o
See code: src/commands/assembly/add-from-gff.ts
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 checks 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
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
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
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
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
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`
- rootPassword:
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
Export the annotations for an assembly to stdout as gff3
USAGE
$ apollo export gff3 ASSEMBLY [--profile <value>] [--config-file <value>] [--include-fasta]
ARGUMENTS
ASSEMBLY Export annotations for this assembly name or id
FLAGS
--config-file=<value> Use this config file (mostly for testing)
--include-fasta Include fasta sequence in output
--profile=<value> Use credentials from this profile
DESCRIPTION
Export the annotations for an assembly to stdout as gff3
EXAMPLES
Export annotations for myAssembly:
$ apollo export gff3 myAssembly > out.gff3
See code: src/commands/export/gff3.ts
Add one or more features to Apollo
USAGE
$ apollo feature add [FEATURE-JSON] [--profile <value>] [--config-file <value>] [-a <value>] [-r <value> -s
<value> -e <value> -t <value>] [-F <value>]
ARGUMENTS
FEATURE-JSON Inline JSON describing the feature(s) to add. Can also be provided via stdin.
FLAGS
-F, --feature-json-file=<value> File with JSON describing the feature(s) to add
-a, --assembly=<value> Name or ID of target assembly. Not required if refseq is unique in the database
-e, --max=<value> End position in target reference sequence
-r, --refSeq=<value> Name or ID of target reference sequence
-s, --min=<value> Start position in target reference sequence
-t, --type=<value> Type of child feature
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Add one or more features to Apollo
A single simple feature can be added using the --min, --max, etc. flags.
To add multiple features, features with more details, or features with children, you can pass in JSON via argument or
stdin or use the --feature-json-file options.
EXAMPLES
Add a single feature by specifying its location and type
$ apollo feature add --assembly hg19 --refSeq chr3 --min 1000 --max 5000 --type remark
Add a single feature from inline JSON
$ apollo feature add \
'{"assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":1,"max":100,"type":"<featureType>"}'
Add mutilple features from stdin JSON
echo '[{"assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":1,"max":100,"type":"<featureType>"},{" \
assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":101,"max":200,"type":"<featureType>"}]' | \
apollo feature add
Add a feature with children from inline JSON
$ apollo feature add '{"assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":1,"max":100,"type":"<fe \
atureType>","children":[{"min":1,"max":50,"type":"<featureType>"}]}'
See code: src/commands/feature/add.ts
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 660...73f -t exon -s 10 -e 20
See code: src/commands/feature/add-child.ts
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
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. The 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
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
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
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
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
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
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
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
Get features given an indexed identifier
USAGE
$ apollo feature get-indexed-id ID [--profile <value>] [--config-file <value>] [-a <value>] [--topLevel]
ARGUMENTS
ID Indexed identifier to search for
FLAGS
-a, --assembly=<value>... Assembly names or IDs to search; use "-" to read it from stdin. If omitted search all
assemblies
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
--topLevel Return the top-level parent of the feature instead of the feature itself
DESCRIPTION
Get features given an indexed identifier
Get features that match a given indexed identifier, such as the ID of a feature from an imported GFF3 file
EXAMPLES
Get features for this indexed identifier:
$ apollo feature get-indexed-id -i abc...zyz def...foo
See code: src/commands/feature/get-indexed-id.ts
Import features from local gff file
USAGE
$ apollo feature import INPUT-FILE -a <value> [--profile <value>] [--config-file <value>] [-d] [--no-strict]
ARGUMENTS
INPUT-FILE Input gff file
FLAGS
-a, --assembly=<value> (required) Import into this assembly name or assembly ID
-d, --delete-existing Delete existing features before importing
--config-file=<value> Use this config file (mostly for testing)
--no-strict If any lines in the GFF3 can't be processed, skip them instead of aborting the import
--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 features.gff3 -d -a myAssembly
See code: src/commands/feature/import.ts
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
Delete files from the Apollo server
USAGE
$ apollo file delete [--profile <value>] [--config-file <value>] [-i <value>]
FLAGS
-i, --file-id=<value>... [default: -] IDs of the files to delete
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Delete files from the Apollo server
Deleted files are printed to stdout. See also `apollo file get` to list the files on the server
EXAMPLES
Delete file multiple files:
$ apollo file delete -i 123...abc xyz...789
See code: src/commands/file/delete.ts
Download a file from the Apollo server
USAGE
$ apollo file download [--profile <value>] [--config-file <value>] [-i <value>] [-o <value>]
FLAGS
-i, --file-id=<value> [default: -] ID of the file to download
-o, --output=<value> Write output to this file or "-" for stdout. Default to the name of the uploaded file.
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Download a file from the Apollo server
See also `apollo file get` to list the files on the server
EXAMPLES
Download file with id xyz
$ apollo file download -i xyz -o genome.fa
See code: src/commands/file/download.ts
Get list of files uploaded to the Apollo server
USAGE
$ apollo file get [--profile <value>] [--config-file <value>] [-i <value>]
FLAGS
-i, --file-id=<value>... Get files matching this IDs
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Get list of files uploaded to the Apollo server
Print to stdout the list of files in json format
EXAMPLES
Get files by id:
$ apollo file get -i xyz abc
See code: src/commands/file/get.ts
Upload a local file to the Apollo server
USAGE
$ apollo file upload INPUT-FILE [--profile <value>] [--config-file <value>] [-t
text/x-fasta|text/x-gff3|application/x-bgzip-fasta|text/x-fai|application/x-gzi] [-z | -d]
ARGUMENTS
INPUT-FILE Local file to upload
FLAGS
-d, --decompressed Override autodetection and instruct that input is decompressed
-t, --type=<option> Set file type or autodetected it if not set.
NB: There is no check for whether the file complies to this type
<options: text/x-fasta|text/x-gff3|application/x-bgzip-fasta|text/x-fai|application/x-gzi>
-z, --gzip Override autodetection and instruct that input is gzip compressed
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Upload a local file to the Apollo server
This command only uploads a file and returns the corresponding file id.
To add an assembly based on this file or to upload & add an assembly in a single pass see `apollo assembly
add-from-fasta` and `add-from-gff`
EXAMPLES
Upload local file, type auto-detected:
$ apollo file upload genome.fa > file.json
See code: src/commands/file/upload.ts
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
Generate JBrowse file for use with desktop client
USAGE
$ apollo jbrowse desktop JBROWSEFILE [--profile <value>] [--config-file <value>] [-o | -w <value>] [-f <value>]
ARGUMENTS
JBROWSEFILE Generated JBrowse file
FLAGS
-f, --gff3-file=<value> generated session will open the specified file
-o, --open open generated file
-w, --open-with=<value> open generated file with specified application
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Generate JBrowse file for use with desktop client
Generates a file that can be opened with JBrowse Desktop. This file has Apollo already configured and, optionally, a
GFF3 for local editing configured as well.
EXAMPLES
Generate JBrowse file:
$ apollo jbrowse desktop apollo.jbrowse
Generate JBrowse file and open with default handler:
$ apollo jbrowse desktop apollo.jbrowse --open
Generate JBrowse file and open with specified application:
$ apollo jbrowse desktop apollo.jbrowse --open-with=path/to/jbrowse.AppImage
Generate JBrowse file opening specified gff3 file:
$ apollo jbrowse desktop apollo.jbrowse --gff3-file=path/to/file.gff3
See code: src/commands/jbrowse/desktop.ts
Get JBrowse configuration from Apollo
USAGE
$ apollo jbrowse get-config [--profile <value>] [--config-file <value>]
FLAGS
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Get JBrowse configuration from Apollo
Print to stdout the JBrowse configuration from Apollo in JSON format
EXAMPLES
Get JBrowse configuration:
$ apollo jbrowse get-config > config.json
See code: src/commands/jbrowse/get-config.ts
Set JBrowse configuration
USAGE
$ apollo jbrowse set-config INPUTFILE [--profile <value>] [--config-file <value>]
ARGUMENTS
INPUTFILE JBrowse configuration file
FLAGS
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Set JBrowse configuration
Set JBrowse configuration in Apollo collaboration server
EXAMPLES
Add JBrowse configuration:
$ apollo jbrowse set-config config.json
See code: src/commands/jbrowse/set-config.ts
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
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
Add reference name aliases from a file
USAGE
$ apollo refseq add-alias INPUT-FILE -a <value> [--profile <value>] [--config-file <value>]
ARGUMENTS
INPUT-FILE Input refname alias file
FLAGS
-a, --assembly=<value> (required) Name for this assembly.
--config-file=<value> Use this config file (mostly for testing)
--profile=<value> Use credentials from this profile
DESCRIPTION
Add reference name aliases from a file
Reference name aliasing is a process to make chromosomes that are named slightly differently but which refer to the
same thing render properly. This command reads a file with reference name aliases and adds them to the database.
EXAMPLES
Add reference name aliases:
$ apollo refseq add-alias alias.txt -a myAssembly
See code: src/commands/refseq/add-alias.ts
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
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
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