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config.js
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config.js
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const BLAST_SEQ_PATH = '/Users/vgs417/blast/seq/';
const BLAST_DATABASE_PATH = '/Users/vgs417/blast/db/';
const DATABASE_NAME_COI = 'bold_COI5P_99_consensus_2024_07_19.fasta' // 'bold_COI5P_99_consensus_2024_01_06.fasta'; //'bold_COI5P_99_consensus_2023_03_12.fasta'; // 'bold_COI5P_99_consensus_2022_02_22.fasta'; // 'bold_COI5P_99_consensus_2021_03_18.fasta'; //'bold_COI5P_99_consensus.fasta';
const DATABASE_NAME_ITS = 'sh_general_release_dynamic_s_all_25.07.2023.fasta'; // 'sh_general_release_dynamic_s_all_29.11.2022.fasta'; //'sh_general_release_dynamic_s_04.02.2020.fasta';
const DATABASE_NAME_16S = 'gtdb_ssu_reps_r214.fasta'; // 'gtdb_ssu_reps_r207.fasta'; //'gtdb_ssu_reps_r202.fasta'; // 'gtdb_ssu_reps_r95.fasta';
const DATABASE_NAME_12S = 'mitofish.12S.Dec2023.fasta'; //'mitofish.12S.May2023.fasta'
const DATABASE_NAME_18S = 'pr2_version_5.0.0_merged.fasta';
const MATCH_THRESHOLD_ITS = 99; // 98.5;
const MATCH_THRESHOLD_COI = 99;
const MATCH_THRESHOLD_16S = 99;
const MATCH_THRESHOLD_12S = 99;
const MATCH_THRESHOLD_18S = 99;
const MATCH_CLOSE_THRESHOLD = 90;
const SUPPORTED_MARKERS = ['its', 'coi', 'co1', '16s', '12s', '18s'];
const MAX_TARGET_SEQS = 5;
const LIMIT_MAX_TARGET_SEQS = 100;
const MINIMUM_QUERY_COVER = 50;// 80; // Minimum percentage of subject that is included in alignment
const NUM_THREADS = 1; // NUM_THREADS * NUM_CONCURRENT_PROCESSES should be equal to the number of cores available for this service
const NUM_CONCURRENT_PROCESSES = 8;
const CACHE_CONCURRENCY = 50;
const env = process.env.NODE_ENV || 'local';
console.log('ENV: ' + env);
const HBASE = {
hosts: ['uc6n10.gbif.org', 'uc6n11.gbif.org', 'uc6n12.gbif.org' ], //["c4master1-vh.gbif.org", "c4master2-vh.gbif.org", "c3master3-vh.gbif.org"],
port: 31995,
tableName: 'blast_cache'
};
const config = {
local: {
BLAST_SEQ_PATH: BLAST_SEQ_PATH,
BLAST_DATABASE_PATH: BLAST_DATABASE_PATH,
DATABASE_NAME: {'ITS': DATABASE_NAME_ITS, 'COI': DATABASE_NAME_COI, '16S': DATABASE_NAME_16S, '12S': DATABASE_NAME_12S, '18S': DATABASE_NAME_18S },
MATCH_THRESHOLD: {'ITS': MATCH_THRESHOLD_ITS, 'COI': MATCH_THRESHOLD_COI, '16S': MATCH_THRESHOLD_16S, '12S': MATCH_THRESHOLD_12S, '18S': MATCH_THRESHOLD_18S},
MATCH_CLOSE_THRESHOLD: {'ITS': MATCH_CLOSE_THRESHOLD, 'COI': MATCH_CLOSE_THRESHOLD, '16S': MATCH_CLOSE_THRESHOLD, '12S': MATCH_CLOSE_THRESHOLD, '18S': MATCH_CLOSE_THRESHOLD},
SUPPORTED_MARKERS: SUPPORTED_MARKERS,
MAX_TARGET_SEQS: MAX_TARGET_SEQS,
LIMIT_MAX_TARGET_SEQS: LIMIT_MAX_TARGET_SEQS,
MINIMUM_QUERY_COVER: MINIMUM_QUERY_COVER,
NUM_THREADS: NUM_THREADS,
NUM_CONCURRENT_PROCESSES: NUM_CONCURRENT_PROCESSES,
EXPRESS_PORT: 9001,
HBASE: HBASE,
CACHE_CONCURRENCY: CACHE_CONCURRENCY
},
production: {
BLAST_SEQ_PATH: '/home/tsjeppesen/seq/',
BLAST_DATABASE_PATH: '/home/tsjeppesen/',
DATABASE_NAME: {'ITS': DATABASE_NAME_ITS, 'COI': DATABASE_NAME_COI, '16S': DATABASE_NAME_16S, '12S': DATABASE_NAME_12S, '18S': DATABASE_NAME_18S },
MATCH_THRESHOLD: {'ITS': MATCH_THRESHOLD_ITS, 'COI': MATCH_THRESHOLD_COI, '16S': MATCH_THRESHOLD_16S, '12S': MATCH_THRESHOLD_12S, '18S': MATCH_THRESHOLD_18S},
MATCH_CLOSE_THRESHOLD: {'ITS': MATCH_CLOSE_THRESHOLD, 'COI': MATCH_CLOSE_THRESHOLD, '16S': MATCH_CLOSE_THRESHOLD, '12S': MATCH_CLOSE_THRESHOLD, '18S': MATCH_CLOSE_THRESHOLD},
SUPPORTED_MARKERS: SUPPORTED_MARKERS,
MAX_TARGET_SEQS: MAX_TARGET_SEQS,
LIMIT_MAX_TARGET_SEQS: LIMIT_MAX_TARGET_SEQS,
MINIMUM_QUERY_COVER: MINIMUM_QUERY_COVER,
NUM_THREADS: NUM_THREADS,
NUM_CONCURRENT_PROCESSES: NUM_CONCURRENT_PROCESSES,
EXPRESS_PORT: 80,
HBASE: HBASE,
CACHE_CONCURRENCY: CACHE_CONCURRENCY
}
};
module.exports = config[env];