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README.md

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Miminal requirements:

  • Linux environment
  • Singularity-CE
  • Postgresql server

Quick Installation & Run:

Set up:

  • Create a postgres database and keep your user/password/host/port and database name handy
  • Please modify the following variables in setenv.sh located in BACKEND/SCRIPT/SHELL/:
    • TG_DIR: Path to the root directory of BioRels
    • PGPASSWORD=Postgres password
    • PGUSER=Postgres user
    • DB_HOST=Postgres host
    • DB_PORT=Postgres port
    • DB_NAME=Database name
    • DB_SCHEMA=Database schema
    • If you are behind a proxy, please set up the proxy variables accordingly.
  • Please execute the following command to load the environment variables:
source BACKEND/SCRIPT/SHELL/setenv.sh

You can check this was successful by running echo $TG_DIR to confirm the root path is set

Compile singularity container

Please run the following command:

cd $TG_DIR/BACKEND/CONTAINER
singularity build biorels_container.sif biorels.sing.txt

This will create a container, called biorels_container.sif that contains all of the 3rd party tools necessary

Quick install and configuration

Please go to $TG_DIR/BACKEND/INSTALL and run the following commands:

biorels_php runInstall.php

And follow the instructions. Please execute the following file:

cp QUICKSTART/CONFIG_USER $TG_DIR/BACKEND/SCRIPT/CONFIG/

This will set up the system to process the following data sources:

  • Taxonomy
  • NCBI Gene (Only Homo sapiens genes)
  • Gene Ontology
  • Sequence, ECO, EFO, Bioassay, MONDO Ontologies
  • SwissLipids
  • Cellausorus
  • Gene Reviews
  • LiverTox

Execution

While still in $TG_DIR/BACKEND/INSTALL, please execute the following command:

biorels_php gen_single_script.php > biorels_execute.sh
sh biorels_execute.sh

This will execute the necessary scripts in the correct order. It will take about an hour and a half.

Querying the database

Please go to

cd $TG_DIR/BACKEND/SCRIPT/API

 biorels_php biorels_api.php  get_taxon_by_tax_id -TAX_ID 9606
 biorels_php biorels_api.php  get_taxon_by_scientific_name -SCIENTIFIC_NAME "Homo sapiens"
 biorels_php biorels_api.php get_chromosome_for_taxon -TAX_ID 9606
 biorels_php biorels_api.php get_gene_for_chromosome -TAX_ID 9606 -CHROMOSOME 1
 biorels_php biorels_api.php get_gene_location -GENE_ID 1017
 biorels_php biorels_api.php get_cell_info -ACC 'CVCL_B6YM'
 biorels_php biorels_api.php search_cell_line_by_disease -DISEASE_TAG 'MONDO_0009692'
 biorels_php biorels_api.php search_gene_ontology -AC 'GO:0010389'
 biorels_php biorels_api.php get_child_gene_ontology -AC 'GO:0010389' -MAX_LEVEL 4

Exporting & Importing:

Please go to

cd $TG_DIR/BACKEND/SCRIPT/BIORJ/

You can execute the following scripts:

 biorels_php api_import.php --JSON Example/HeLa.biorj
 biorels_php api_export.php -JSON_OUTPUT=CVCL_B6YM.biorj --JSON_PRETTY_PRINT CELL CVCL_B6YM && more CVCL_B6YM.biorj
 biorels_php api_import.php --JSON Example/rs712.json