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local.cfg
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49 lines (45 loc) · 1.37 KB
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import glob
import os
DB_HOST='localhost'
DB_PORT=27017
DB_NAME='uclex'
DB_NAME_HPO='hpo'
DB_NAME_PATIENTS='patients'
DB_NAME_USERS='users'
DB_NAME_CACHE='cache'
DEBUG=True
DEBUG_TB_TEMPLATE_EDITOR_ENABLED=True
#SECRET_KEY='development key'
UCLEX_FILES_DIRECTORY=''
# contigs assigned to threads, so good to make this a factor of 24 (eg. 2,3,4,6,8)
LOAD_DB_PARALLEL_PROCESSES = 4
SITES_VCFS=''
GENCODE_GTF=''
CANONICAL_TRANSCRIPT_FILE=''
OMIM_FILE=''
BASE_COVERAGE_FILES=''
DBNSFP_FILE=''
CONSTRAINT_FILE=''
MNP_FILE=''
# How to get a dbsnp142.txt.bgz file:
# wget ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b142_GRCh37p13/database/organism_data/b142_SNPChrPosOnRef_105.bcp.gz
# zcat b142_SNPChrPosOnRef_105.bcp.gz | awk '$3 != ""' | perl -pi -e 's/ +/\t/g' | sort -k2,2 -k3,3n | bgzip -c > dbsnp142.txt.bgz
# tabix -s 2 -b 3 -e 3 dbsnp142.txt.bgz
DBSNP_FILE=''
READ_VIZ_DIR=''
GENE_CACHE_DIR =''
GENES_TO_CACHE = ''
HPO_OBO= ''
RETNET_KNOWN_GENES='offline_analysis/gene_list/retnet_known_genes.txt'
RETNET_JSON='offline_analysis/gene_list/retnet.json'
# pubmedBatch field defaults
PUBMED_EMAIL='[email protected]'
PUBMEDBATCH_OR='retina retinal retinitis blindness macula macular stargardt'
# pubmedBatch search lifetime in second. 2592000 = 30 days
PUBMEDBATCH_LIFE=2592000
DEFAULT_USER='Jing'
HTML_COMPRESS=True
# Neo4j
NEO4J_HOST='localhost'
NEO4J_BOLT_PORT= 7687
NEO4J_PWD='1'