Command Line Reference

This page provides brief descriptions of all the ImmuneDB commands and the default help text for each. For a step-by-step guide to running the pipeline, refer to Running the Data Analysis Pipeline.

immunedb_admin

Manages ImmuneDB instances.

usage: immunedb_admin [-h] {create,delete,backup,restore} ...

Administrative tools for ImmuneDB database instances

positional arguments:
  {create,delete,backup,restore}
                        The task to begin
    create              Creates a new ImmuneDB database
    delete              Deletes an existing ImmuneDB database
    backup              Backs up an ImmuneDB database
    restore             Restores a backup of an ImmuneDB database

optional arguments:
  -h, --help            show this help message and exit

immunedb_admin create

Creates a new ImmuneDB instance.

usage: immunedb_admin create [-h] [--db-host DB_HOST] [--db-user DB_USER]
                             [--db-pass] [--admin-user ADMIN_USER]
                             [--admin-pass ADMIN_PASS]
                             db_name config_dir

positional arguments:
  db_name               Database name (letters, numbers, dashes and
                        underscores only)
  config_dir            The directory in which to store the generated
                        configuration file.

optional arguments:
  -h, --help            show this help message and exit
  --db-host DB_HOST     Hostname or IP of the MySQL server.
  --db-user DB_USER     Name of MySQL user to generate for the database.
  --db-pass             Prompt for MySQL user password.
  --admin-user ADMIN_USER
                        MySQL user with rights to create databases.
  --admin-pass ADMIN_PASS
                        Specify the admin password at the command line instead
                        of prompting.

immunedb_admin delete

Deletes an ImmuneDB instance.

usage: immunedb_admin delete [-h] [--delete-user] [--admin-user ADMIN_USER]
                             [--admin-pass ADMIN_PASS]
                             db_config

positional arguments:
  db_config             Path to database config

optional arguments:
  -h, --help            show this help message and exit
  --delete-user         If specified will also delete the user associated with
                        the database. Deleting the user will also delete it
                        for other database, so only use if you're deleting
                        those other databases or the user is only associated
                        with this database.
  --admin-user ADMIN_USER
                        MySQL user with rights to create databases.
  --admin-pass ADMIN_PASS
                        Specify the admin password at the command line instead
                        of prompting.

immunedb_admin backup

Performs a SQL dump from a ImmuneDB instance, backing up the contents.

usage: immunedb_admin backup [-h] db_config backup_path

positional arguments:
  db_config    Path to database config
  backup_path  Path to backup file

optional arguments:
  -h, --help   show this help message and exit

immunedb_admin restore

Restores a SQL dump from immunedb_admin backup.

usage: immunedb_admin restore [-h] db_config backup_path

positional arguments:
  db_config    Path to database config
  backup_path  Path to backup file

optional arguments:
  -h, --help   show this help message and exit

immunedb_clone_import

Imports custom clonal assignments from an exported sequence template.

To use, run immunedb_clone_import ... --action export, fill in the clone_id column for each sequence, then run immunedb_clone_import ... --action import. All sequences assigned to a given clone must have the same V-gene, J-gene, and CDR3 length, otherwise an error will be raised.

usage: immunedb_clone_import [-h] --action {import,export} [--regen]
                             db_config file

Allows for importing of clone associations

positional arguments:
  db_config             Path to database config
  file

optional arguments:
  -h, --help            show this help message and exit
  --action {import,export}
  --regen               If all existing clones should be deleted. Will also
                        delete all clone stats and sample stats (default:
                        False)

immunedb_clone_pressure

Note

For selection pressure calculations, BASELINe must be installed.

Calculates the selection pressure acting on clonal sequences.

usage: immunedb_clone_pressure [-h] [--nproc NPROC]
                               [--clone-ids CLONE_IDS [CLONE_IDS ...]]
                               [--subject-ids SUBJECT_IDS [SUBJECT_IDS ...]]
                               [--regen] [--temp TEMP]
                               [--thresholds THRESHOLDS [THRESHOLDS ...]]
                               db_config baseline_path

Calculates clonal selection pressure

positional arguments:
  db_config             Path to database config
  baseline_path         Path to Baseline main script.

optional arguments:
  -h, --help            show this help message and exit
  --nproc NPROC         Number of subprocesses to run (Default: 12) (default:
                        12)
  --clone-ids CLONE_IDS [CLONE_IDS ...]
                        Limit to certain clone IDS (default: None)
  --subject-ids SUBJECT_IDS [SUBJECT_IDS ...]
                        Limit to certain subjects (default: None)
  --regen               Recalculate clone selection pressure even if it
                        already exists (default: False)
  --temp TEMP           Path for temporary baseline files (default: /tmp)
  --thresholds THRESHOLDS [THRESHOLDS ...]
                        Specifies the minimum number(s) of sequences in which
                        mutations must occur to be included in analysis.
                        Multiple values are allowed and will calculate
                        multiple selection pressures. Positive integers
                        indicate the minimum number of sequences. If an
                        argument ends with %, it specifies the minimum
                        percentage of sequences. If an argument ends with E,
                        it specifies the exact number of times the mutation
                        can occur.For example, '--thresholds 1 1E 2 85%"' will
                        calculate selection pressure for mutations occurring
                        at least once (all mutations), exactly once, at least
                        twice, and in at least 85% of sequences. (default:
                        ['1', '2', '85%'])

immunedb_clones

Assigns sequences to clones using one of three methods.

usage: immunedb_clones [-h] [--nproc NPROC]
                       [--subject-ids SUBJECT_IDS [SUBJECT_IDS ...]]
                       [--include-indels] [--exclude-partials]
                       [--min-identity MIN_IDENTITY] [--min-copy MIN_COPY]
                       [--max-padding MAX_PADDING] [--regen] [--subclones]
                       db_config {similarity,tcells,lineage} ...

Clusters sequences into clones

positional arguments:
  db_config             Path to database config
  {similarity,tcells,lineage}
                        The method to use for clonal inference
    similarity          Constructs clones based on CDR3 amino-acid hamming
                        distance
    tcells              Constructs clones based on exact CDR3 NT identity for
                        T-cells
    lineage             Constructs clones based on lineage trees

optional arguments:
  -h, --help            show this help message and exit
  --nproc NPROC         Number of subprocesses to run (Default: 12) (default:
                        12)
  --subject-ids SUBJECT_IDS [SUBJECT_IDS ...]
                        Limit generation to certain subjects (default: None)
  --include-indels      If specified, includes indels (or poorly aligned
                        sequences) in clones. (default: False)
  --exclude-partials    'If specified, excludes partial sequences in clones.
                        Note partial sequences which were collapse to a full
                        sequence will always be included. (default: False)
  --min-identity MIN_IDENTITY
                        Minimum V identity of sequences to germline required
                        for inclusion in clones. (default: 0)
  --min-copy MIN_COPY   The minimum copy number that sequences must have in
                        the subject to be included in clones. (default: 2)
  --max-padding MAX_PADDING
                        Maximum V-padding a sequence may have to be added to a
                        clone. (default: None)
  --regen               If specified all clones (limited by subject if
                        --subject is specified) will be DELETED before
                        creating new clones. Associated sequences will be re-
                        assigned new clones (default: False)
  --subclones           If specified, calculates subclone relationships
                        (default: False)

immunedb_clones similarity

Groups sequences with the same subject, V-gene, J-gene, CDR3 length, and (by default) 85% CDR3 AA similarity into clones.

usage: immunedb_clones db_config similarity [-h]
                                            [--min-similarity MIN_SIMILARITY]

optional arguments:
  -h, --help            show this help message and exit
  --min-similarity MIN_SIMILARITY
                        Minimum similarity allowed between sequence CDR3 AAs
                        within a clone (default: 85)

immunedb_clones tcells

Groups sequences with the same subject, V-gene, J-gene, and CDR3 NT sequence into clones.

usage: immunedb_clones db_config tcells [-h]

optional arguments:
  -h, --help  show this help message and exit

immunedb_clones lineage

Note

To assign clones via the lineage tree method, Clearcut must be installed.

Creates lineages out of all sequences with the same subject, V-gene, J-gene, and CDR3 length. Then, the lineage is split along branches where the aggregate number of mutations is at least --mut-cuttoff (default 4).

usage: immunedb_clones db_config lineage [-h] [--mut-cuttoff MUT_CUTTOFF]
                                         [--min-mut-occurrence MIN_MUT_OCCURRENCE]
                                         [--min-mut-samples MIN_MUT_SAMPLES]
                                         [--min-seq-instances MIN_SEQ_INSTANCES]
                                         clearcut_path

positional arguments:
  clearcut_path         Path to clearcut binary

optional arguments:
  -h, --help            show this help message and exit
  --mut-cuttoff MUT_CUTTOFF
                        The number of mutations allowed along a path in the
                        linage before the linage is split into two clones
                        (default: 4)
  --min-mut-occurrence MIN_MUT_OCCURRENCE
                        The minimum number of times a mutation must occur to
                        be included in the lineage (default: 2)
  --min-mut-samples MIN_MUT_SAMPLES
                        The minimum number of samples in which a mutation must
                        occur to be incorporated into tree calculation
                        (default: 1)
  --min-seq-instances MIN_SEQ_INSTANCES
                        The minimum number of instances a sequence must have
                        to be incorporated into tree calculation (default: 1)

immunedb_clone_stats

Aggregates statistics about clones for quicker, easier bulk querying.

usage: immunedb_clone_stats [-h] [--nproc NPROC]
                            [--clone-ids CLONE_IDS [CLONE_IDS ...]]
                            [--subject-ids SUBJECT_IDS [SUBJECT_IDS ...]]
                            [--regen]
                            db_config

Generates statistics for clones

positional arguments:
  db_config             Path to database config

optional arguments:
  -h, --help            show this help message and exit
  --nproc NPROC         Number of subprocesses to run (Default: 12) (default:
                        12)
  --clone-ids CLONE_IDS [CLONE_IDS ...]
                        Limit to certain clone IDS (default: None)
  --subject-ids SUBJECT_IDS [SUBJECT_IDS ...]
                        Limit to certain subjects (default: None)
  --regen               Regenerates stats even if they already exist (default:
                        False)

immunedb_clone_trees

Note

To create lineage trees, Clearcut must be installed.

Creates a lineage tree for each clone using Neighbor Joining.

usage: immunedb_clone_trees [-h] [--nproc NPROC] [--force]
                            [--clone-ids CLONE_IDS [CLONE_IDS ...]]
                            [--subject-ids SUBJECT_IDS [SUBJECT_IDS ...]]
                            [--temp TEMP] [--min-count MIN_COUNT]
                            [--min-seq-copies MIN_SEQ_COPIES]
                            [--min-samples MIN_SAMPLES] [--exclude-stops]
                            db_config clearcut_path

Generates JSON trees for clones

positional arguments:
  db_config             Path to database config
  clearcut_path         Path to clearcut binary

optional arguments:
  -h, --help            show this help message and exit
  --nproc NPROC         Number of subprocesses to run (Default: 12) (default:
                        12)
  --force               Force updating of trees (default: False)
  --clone-ids CLONE_IDS [CLONE_IDS ...]
                        ID of clone from which to make a tree (default: None)
  --subject-ids SUBJECT_IDS [SUBJECT_IDS ...]
                        ID of subject for which all clones should be make
                        (default: None)
  --temp TEMP           Path for temporaryfiles (default: /tmp)
  --min-count MIN_COUNT
                        The minimum number of times a mutation must occur to
                        be incorporated into tree calculation. (default: 1)
  --min-seq-copies MIN_SEQ_COPIES
                        The minimum copy number a sequence must have to be
                        incorporated into tree calculation. (default: 0)
  --min-samples MIN_SAMPLES
                        The minimum number of samples in which a mutation must
                        occur to be incorporated into tree calculation.
                        (default: 1)
  --exclude-stops       If specified, excludes sequences with a stop codon
                        from being included in trees. (default: False)

immunedb_collapse

Collapses identical sequences across all samples in each subject.

usage: immunedb_collapse [-h] [--nproc NPROC]
                         [--subject-ids SUBJECT_IDS [SUBJECT_IDS ...]]
                         db_config

Collapses sequences at the sample andsubject level.

positional arguments:
  db_config             Path to database config

optional arguments:
  -h, --help            show this help message and exit
  --nproc NPROC         Number of subprocesses to run (Default: 12) (default:
                        12)
  --subject-ids SUBJECT_IDS [SUBJECT_IDS ...]
                        Subject ID(s) to collapse. (default: None)

immunedb_export

Exports data from ImmuneDB into various formats

usage: immunedb_export [-h] db_config {vdjtools,genbank,changeo} ...

Exports ImmuneDB data in various formats

positional arguments:
  db_config             Path to database config
  {vdjtools,genbank,changeo}
                        The format

optional arguments:
  -h, --help            show this help message and exit

immunedb_export changeo

usage: immunedb_export db_config changeo [-h] [--clones-only]
                                         [--min-subject-copies MIN_SUBJECT_COPIES]

optional arguments:
  -h, --help            show this help message and exit
  --clones-only         Includes only sequences assigned to a clone
  --min-subject-copies MIN_SUBJECT_COPIES
                        The minimum copies in the subject required to be
                        exported. Set to 1 for all subject-unique sequences,
                        or higher for more stringent filtering

immunedb_export genbank

usage: immunedb_export db_config genbank [-h] [--inference INFERENCE]
                                         [--gene-db GENE_DB]
                                         [--species SPECIES]
                                         [--mol-type MOL_TYPE]

optional arguments:
  -h, --help            show this help message and exit
  --inference INFERENCE
                        Inference tool used for gene assignment
  --gene-db GENE_DB     Reference V/J gene database
  --species SPECIES     Species of sequences
  --mol-type MOL_TYPE   Molecule type

immunedb_export vdjtools

usage: immunedb_export db_config vdjtools [-h]
                                          [--min-clone-size MIN_CLONE_SIZE]
                                          [--include-uniques]

optional arguments:
  -h, --help            show this help message and exit
  --min-clone-size MIN_CLONE_SIZE
                        Only export clones with at least this many copies.
  --include-uniques     Includes how many unique sequences are in clones.

immunedb_genotype

Note

To genotype subjects, TIgGER must be installed.

Runs genotyping on a database that was generated with immunedb_identify ... --genotyping.

usage: immunedb_genotype [-h] [--nproc NPROC]
                         [--changeo-export-path CHANGEO_EXPORT_PATH]
                         [--subject-ids SUBJECT_IDS [SUBJECT_IDS ...]]
                         [--j-max J_MAX] [--min-seqs MIN_SEQS]
                         [--germline-min GERMLINE_MIN]
                         db_config v_germlines

Runs TIgGER to infer genotypes for subjects

positional arguments:
  db_config             Path to database config
  v_germlines           FASTA file with IMGT gapped V-gene germlines

optional arguments:
  -h, --help            show this help message and exit
  --nproc NPROC         Number of subprocesses to run (Default: 12) (default:
                        12)
  --changeo-export-path CHANGEO_EXPORT_PATH
  --subject-ids SUBJECT_IDS [SUBJECT_IDS ...]
                        Limit to certain subjects (default: None)
  --j-max J_MAX         [TIgGER] Maximum fraction of sequences perfectly
                        aligning to a potential novel allele that are allowed
                        to utilize to a particular combination of junction
                        length and J gene (default: 1.0)
  --min-seqs MIN_SEQS   [TIgGER] Minimum number of total sequences required
                        for the samples to be considered (default: 10)
  --germline-min GERMLINE_MIN
                        [TIgGER] Minimum number of sequences that must have a
                        particular germline allele call for the allele to be
                        analyzed (default: 10)

immunedb_identify

Identifies V- and J-genes of sequences in FASTA/FASTQ files using an `anchor method.

usage: immunedb_identify [-h] [--nproc NPROC]
                         [--upstream-of-cdr3 UPSTREAM_OF_CDR3]
                         [--anchor-len ANCHOR_LEN]
                         [--min-anchor-len MIN_ANCHOR_LEN]
                         [--metadata METADATA] [--max-vties MAX_VTIES]
                         [--min-similarity MIN_SIMILARITY]
                         [--max-padding MAX_PADDING] [--trim-to TRIM_TO]
                         [--warn-existing] [--genotyping]
                         db_config v_germlines j_germlines sample_dir

Identifies V and J genes from FASTA files

positional arguments:
  db_config             Path to database config
  v_germlines           FASTA file with IMGT gapped V-gene germlines
  j_germlines           FASTA file with J-gene germlines. The final nucleotide
                        in all genes must be aligned. Sequence cannot contain
                        any gaps.
  sample_dir            Base directory for samples.

optional arguments:
  -h, --help            show this help message and exit
  --nproc NPROC         Number of subprocesses to run (Default: 12) (default:
                        12)
  --upstream-of-cdr3 UPSTREAM_OF_CDR3
                        The number of nucleotides in the J germlines upstream
                        of the CDR3 (default: 31)
  --anchor-len ANCHOR_LEN
                        The number of nucleotides at the end of the J
                        germlines to use as anchors. (default: 18)
  --min-anchor-len MIN_ANCHOR_LEN
                        The minimum number of nucleotides in the J germline
                        anchors required to match the sequence. (default: 12)
  --metadata METADATA   Path to metadata file. If not specified, expects
                        "metadata.tsv" to exist in the base_dir (default:
                        None)
  --max-vties MAX_VTIES
                        Maximum number of V-ties to allow in a valid sequence.
                        V-ties resulting in a name longer than 512 characters
                        will be truncated. (default: 50)
  --min-similarity MIN_SIMILARITY
                        Minimum fraction similarity to germline required for
                        valid sequences. (default: 0.6)
  --max-padding MAX_PADDING
                        If specified, discards sequences with too much
                        padding. (default: None)
  --trim-to TRIM_TO     If specified, trims the beginning N bases of each
                        sequence. Useful for removing primers within the V
                        sequence. (default: 0)
  --warn-existing       If specified, warns of existing samples and skips
                        them. Otherwise, an error is raised and identification
                        will not begin. (default: False)
  --genotyping          Alters identification to process sequences for
                        genotyping with TIgGER (default: False)

immunedb_import

Note

Importing from a delimited file is still considered in beta and may not work as intended. Please report any bugs on github.

Imports sequence alignments and gene calls from a tab delimited file (by default in IMGT format)

usage: immunedb_import [-h] [--nproc NPROC]
                       [--upstream-of-cdr3 UPSTREAM_OF_CDR3]
                       [--anchor-len ANCHOR_LEN]
                       [--min-anchor-len MIN_ANCHOR_LEN]
                       [--max-padding MAX_PADDING] [--trim-to TRIM_TO]
                       [--remap-js REMAP_JS [REMAP_JS ...]]
                       [--meta META [META ...]]
                       [--full-sequence FULL_SEQUENCE] [--seq-id SEQ_ID]
                       [--copy-number COPY_NUMBER] [--j-gene J_GENE]
                       [--v-gene V_GENE]
                       db_config input_file v_germlines j_germlines

Imports V/J identifications from delimited output

positional arguments:
  db_config             Path to database config
  input_file            Gapped NT file
  v_germlines           FASTA file with IMGT gapped V-gene germlines
  j_germlines           FASTA file with J-gene germlines. The final nucleotide
                        in all genes must be aligned. Sequence cannot contain
                        any gaps.

optional arguments:
  -h, --help            show this help message and exit
  --nproc NPROC         Number of subprocesses to run (Default: 12) (default:
                        12)
  --upstream-of-cdr3 UPSTREAM_OF_CDR3
                        The number of nucleotides in the J germlines upstream
                        of the CDR3 (default: 31)
  --anchor-len ANCHOR_LEN
                        The number of nucleotides at the end of the J
                        germlines to use as anchors. (default: 18)
  --min-anchor-len MIN_ANCHOR_LEN
                        The minimum number of nucleotides in the J germline
                        anchors required to match the sequence. (default: 12)
  --max-padding MAX_PADDING
                        If specified, discards sequences with too much
                        padding. (default: None)
  --trim-to TRIM_TO     If specified, trims the beginning N bases of each
                        sequence. Useful for removing primers within the V
                        sequence. (default: 0)
  --remap-js REMAP_JS [REMAP_JS ...]
                        Remaps J genes to others in the germline file. Format
                        is FROM:TO[ FROM:TO[...]]. For example IGHJ1:IGHJ2
                        will remap any IGHJ1 gene to IGHJ2. The FROM gene can
                        be a prefix but TO must be the full gene name
                        (default: None)
  --meta META [META ...]
                        Additional metadata for the sample. Must be in the
                        format KEY=VALUE (e.g. --meta tissue=Spleen). May be
                        specified multiple times (default: None)
  --full-sequence FULL_SEQUENCE
                        Header for full_sequence (Default: V-D-J-REGION)
                        (default: V-D-J-REGION)
  --seq-id SEQ_ID       Header for seq_id (Default: Sequence ID) (default:
                        Sequence ID)
  --copy-number COPY_NUMBER
                        Header for copy_number (default: None)
  --j-gene J_GENE       Header for j_gene (Default: J-GENE and allele)
                        (default: J-GENE and allele)
  --v-gene V_GENE       Header for v_gene (Default: V-GENE and allele)
                        (default: V-GENE and allele)

immunedb_local_align

Note

To locally align sequences Bowtie2 must be installed.

Corrects sequences that were flagged as potential indels or unidentifiable by immunedb_identify. This can be a slow process for large datasets.

usage: immunedb_local_align [-h] [--nproc NPROC] [--temp TEMP]
                            [--upstream_of_cdr3 UPSTREAM_OF_CDR3]
                            [--max-deletions MAX_DELETIONS]
                            [--max-insertions MAX_INSERTIONS]
                            [--max-vties MAX_VTIES]
                            [--min-similarity MIN_SIMILARITY]
                            [--max-padding MAX_PADDING] [--trim-to TRIM_TO]
                            db_config v_germlines j_germlines

Attempts to locally align sequences that could not be properly aligned with
the anchoring method.

positional arguments:
  db_config             Path to database config
  v_germlines           FASTA file with IMGT gapped V-gene germlines
  j_germlines           FASTA file with J-gene germlines. The final nucleotide
                        in all genes must be aligned. Sequence cannot contain
                        any gaps.

optional arguments:
  -h, --help            show this help message and exit
  --nproc NPROC         Number of subprocesses to run (Default: 12) (default:
                        12)
  --temp TEMP           Path for temporary files (default: /tmp)
  --upstream_of_cdr3 UPSTREAM_OF_CDR3
                        The number of nucleotides in the J germlines upstream
                        of the CDR3 (default: 31)
  --max-deletions MAX_DELETIONS
                        Maximum number of deletion blocks allowed. (default:
                        3)
  --max-insertions MAX_INSERTIONS
                        Maximum number of insertion blocks allowed. (default:
                        3)
  --max-vties MAX_VTIES
                        Maximum number of V-ties to allow in a valid sequence.
                        V-ties resulting in a name longer than 512 characters
                        will be truncated. (default: 50)
  --min-similarity MIN_SIMILARITY
                        Minimum fraction similarity to germline required for
                        valid sequences. (default: 0.6)
  --max-padding MAX_PADDING
                        If specified discards sequences with too much padding.
                        (default: None)
  --trim-to TRIM_TO     If specified, trims the beginning N bases of each
                        sequence. Useful for removing primers within the V
                        sequence. (default: 0)

immunedb_metadata

Generates metadata for a set of FASTA/FASTQ files to use for immunedb_identify.

usage: Generates a template metadata file [-h] [--path PATH] [--out OUT]
                                          [--use-filenames] [--include-common]

optional arguments:
  -h, --help        show this help message and exit
  --path PATH       The directory in which the FASTA or FASTQ files exist.
  --out OUT         Path to output file. Use - for stdout.
  --use-filenames   Sets the sample name for each file to the filename without
                    the .fasta or .fastq extension (e.g. sample1.fasta would
                    be given the sample name sample1)
  --include-common  Includes additional common metadata fields: date,subset,ti
                    ssue,disease,lab,experimenter,ig_class,timepoint,v_primer,
                    j_primer

immunedb_rest

Starts a REST API server for ImmuneDB. This can be used for any purpose, but is designed to provide data for the ImmuneDB Frontend.

usage: immunedb_rest [-h] [--nproc NPROC] [-p PORT] [-d] [--allow-shutdown]
                     [--rollbar-token ROLLBAR_TOKEN]
                     [--rollbar-env ROLLBAR_ENV]
                     db_config

Provides a restless interface to thedatabase

positional arguments:
  db_config             Path to database config

optional arguments:
  -h, --help            show this help message and exit
  --nproc NPROC         Number of subprocesses to run (Default: 12) (default:
                        12)
  -p PORT               API offer port (default: 5000)
  -d                    Use debug mode (default: False)
  --allow-shutdown      Allows remote shutdown by accessing /shutdown. Only
                        use during testing! (default: False)
  --rollbar-token ROLLBAR_TOKEN
                        Token for rollbar reporting (default: None)
  --rollbar-env ROLLBAR_ENV
                        Environment for rollbar reporting (default: develop)

immunedb_sample_stats

Calculates aggregate statistics for samples for faster querying.

usage: immunedb_sample_stats [-h] [--nproc NPROC]
                             [--sample-ids SAMPLE_IDS [SAMPLE_IDS ...]]
                             [--force]
                             db_config

Generates statistics for samples

positional arguments:
  db_config             Path to database config

optional arguments:
  -h, --help            show this help message and exit
  --nproc NPROC         Number of subprocesses to run (Default: 12) (default:
                        12)
  --sample-ids SAMPLE_IDS [SAMPLE_IDS ...]
                        Limit statistics updates to certain samples (default:
                        None)
  --force               Force regeneration of stats even if they already exist
                        (default: False)

immunedb_sql

Starts an interactive MySQL session for a given ImmuneDB instance. This is simply a wrapper around the mysql command that passes information from a configuration file.

usage: immunedb_sql [-h] db_config

Starts a MySQL CLI session from a configuration file

positional arguments:
  db_config   Path to database config

optional arguments:
  -h, --help  show this help message and exit