DAE Configuration

This is the main configuration file - it lists GPF subsystems in the form of sections and specifies required parameters, such as the location of a configuration file and other filesystem paths.

Note

You can use interpolation values when specifying filepaths.

Parser

DAEConfigParser is the parser responsible for reading and parsing this configuration file.

Example Configuration

[DEFAULT]
instance_id = data_hg19_startup

[genotype_storage]
default = genotype_impala

[storage.genotype_impala]
type = impala
impala.host = localhost
impala.port = 21050
impala.db = gpf_variant_db
hdfs.host = localhost
hdfs.port = 8020
hdfs.base_dir = /user/%(instance_id)s/studies

[storage.genotype_filesystem]
type = filesystem
dir = %(wd)s/studies

[studiesDB]
confFile = %(wd)s/studiesDB.conf
dir = %(wd)s/studies

[datasetsDB]
confFile = %(wd)s/datasetsDB.conf
dir = %(wd)s/datasets

[genomesDB]
confFile = %(wd)s/genomesDB.conf

[genomicScoresDB]
confFile = %(wd)s/genomicScores.conf
scores_hg19_dir = /genomic-scores-hg19
scores_hg38_dir = /genomic-scores-hg38

[annotation]
confFile = %(wd)s/annotation.conf

[phenoDB]
dir = %(wd)s/pheno

[geneInfoDB]
confFile = %(wd)s/geneInfo.conf

[defaultConfiguration]
confFile = %(wd)s/defaultConfiguration.conf

[gpfjs]
permissionDeniedPrompt = This is a default permission denied prompt. Please log in or register.
permissionDeniedPromptFile = %(wd)s/permissionDeniedPrompt.md

[genotype_storage]

default

default = <default genotype storage id>

The default genotype storage to use. The genotype storage id must reference a configured genotype storage from one of the [storage.<genotype storage id>] sections below.

[storage.<genotype storage id>]

type

type = <genotype storage type>

Type of the genotype storage. Supported types are impala and filesystem.

impala genotype storage options

impala.host

impala.host = <Impala hostname>
ENVIRONMENT OVERRIDE

DAE_IMPALA_HOST

Hostname of the Impala server.

impala.port

impala.port = <Impala port number>
DEFAULT

21050

ENVIRONMENT OVERRIDE

DAE_IMPALA_PORT

Port number of the Impala server.

impala.db

impala.db = <Impala database name>
DEFAULT

gpf_variant_db

ENVIRONMENT OVERRIDE

DAE_IMPALA_DB

Name of the database used by Impala for storing variants and pedigree information.

hdfs.host

hdfs.host = <HDFS hostname>
ENVIRONMENT OVERRIDE

DAE_HDFS_HOST

Hostname of the HDFS server.

hdfs.port

hdfs.port = <HDFS port number>
DEFAULT

0

ENVIRONMENT OVERRIDE

DAE_HDFS_PORT

Port number of the HDFS server.

hdfs.base_dir

hdfs.base_dir = <>
DEFAULT

/tmp

filessytem genotype storage options

dir

dir = <directory containing studies>

Directory containing studies data.

[studiesDB]

confFile

confFile = <studies db config file>

The absolute filepath to the studiesDB configuration file. You can see more about this configuration here.

dir

dir = <directory containing studies>

Directory containing studies data. This directory is expected to contain study configurations. You can see more about study and dataset configurations here.

[datasetsDB]

confFile

confFile = <datasets db config file>

The absolute filepath to the datasetsDB configuration file. You can see more about this configuration here.

dir

dir = <directory containing datasets>

Directory containing datasets data. This directory is expected to contain dataset configurations. You can see more about study and dataset configurations here.

[genomesDB]

confFile

confFile = <genomes db config file path>

The absolute filepath to the genomesDB configuration file. You can see more about this configuration here.

[genomicScoresDB]

confFile

confFile = <genomic scores db file path>

The absolute filepath to the genomicScoresDB configuration file. You can see more about this configuration here.

scores_hg19_dir

scores_hg19_dir = <dir containing HG19 genomic scores>
ENVIRONMENT OVERRIDE

DAE_GENOMIC_SCORES_HG19

The absolute path to the directory containing the HG19 genomic scores.

scores_hg38_dir

scores_hg38_dir = <dir containing HG38 genomic scores>
ENVIRONMENT OVERRIDE

DAE_GENOMIC_SCORES_HG38

The absolute path to the directory containing the HG38 genomic scores.

[annotation]

confFile

confFile = <annotation configuration file path>

The absolute filepath to the annotation configuration file. You can see more about this configuration here.

[phenoDB]

dir

dir = <phenotype databases directory>

The absolute filepath to the directory containing phenotype databases. The system will traverse this path and load any INI configuration files that contain a phenoDB section. You can see more about phenotype database configurations here.

[geneInfoDB]

confFile

confFile = <gene info db configuration file path>

The absolute filepath to the geneInfoDB configuration file. You can see more about this configuration here.

[defaultConfiguration]

confFile

confFile = <defaultConfiguration file path>

The absolute filepath to the defaultConfiguration file. The configuration in this file is used as a default configuration for all studies and datasets. You can see more about this configuration here.

[gpfjs]

permissionDeniedPromptFile

permissionDeniedPromptFile = <absolute filepath to markdown file>

The absolute filepath to the permissionDeniedPromptFile file. This file contains markdown to display in the browser when access is denied to a user. The content of this file is stored in permissionDeniedPrompt.

permissionDeniedPrompt

permissionDeniedPrompt = <markdown>
DEFAULT

This is a default permission denied prompt. Please log in or register.

The markdown to display in the browser when access to a user is denied. If permissionDeniedPromptFile is defined, this property is overridden with the file content from the given path.