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
- ENVIRONMENT OVERRIDE
DAE_IMPALA_PORT
Port number of the Impala server.
impala.db
impala.db = <Impala database name>
- DEFAULT
- 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
- ENVIRONMENT OVERRIDE
DAE_HDFS_PORT
Port number of the HDFS server.
hdfs.base_dir
hdfs.base_dir = <>
- DEFAULT
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
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.