biggr_models/settings.ini.docker at main · biosustain/biggr_models · GitHub

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[GENERAL]
# Number of processes for parallelization
n_processes = 4

[DATABASE]
# Set host here or set environment variable COBRADB_POSTGRES_HOST
postgres_host = biggr-db

# Set port here or set environment variable COBRADB_POSTGRES_PORT
postgres_port = 5432

# Set user here or set environment variable COBRADB_POSTGRES_USER
postgres_user = biggr

# Set password here or set environment variable COBRADB_POSTGRES_PASSWORD
postgres_password = POSTGRESDOCKERPASSWORD

# Set database here or set environment variable COBRADB_POSTGRES_DATABASE
postgres_database = biggr

# Set test database here or set environment variable
# COBRADB_POSTGRES_TEST_DATABASE
postgres_test_database = cobradb_test

[DATA]
# The directory containing the genome-scale models
# model_directory = /app/bigg_models_data/models
model_directory = /input_models

# The directory containing the reference sequences (as Genbank files)
# refseq_directory = /genbank
refseq_directory = /assemblies

# A tab-delimited text file containing models, reference sequences, and
# publication IDs
# model_genome = /app/bigg_models_data/model-genome-iml1515.tsv
# model_genome = /app/bigg_models_data/model-genome-small_set.tsv
# model_genome = /app/model-genome-small_set_2.tsv
# model_genome = /app/model-genome-small_set_4.json
model_genome = /app/model-genome-set-6.json
# model_genome = /app/model-genome-iML1515.json

# A tab-delimited text file containing compartment IDs and their corresponding
# names
compartment_names = /datafiles/compartment-names.txt
data_source_preferences = /app/bigg_models_data/data-source-prefs.txt

taxonomy_nodes = /datafiles/nodes.dmp
taxonomy_names = /datafiles/names.dmp

rhea = /datafiles/rhea.ttl

curated_metabolites = /datafiles/bigg_id_data.json

curated_reactions = /datafiles/reaction_data.json

default_chebis = /datafiles/chebi_pH7_3_mapping.tsv

chebi_cache_dir = /chebi/