Build ChEMBL for SEA - Revision history

Khtang: /* Setting up Postgres */

2023-06-22T21:19:51Z

Setting up Postgres

← Older revision		Revision as of 21:19, 22 June 2023
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	- To list all schemas: \dn		- To list all schemas: \dn
	- To view table setup: \d+ <table_name>		- To view table setup: \d+ <table_name>
			In Postgresql console:
			Create new schema
			CREATE SCHEMA chembl33;
			Change default schema to the newly created one, you must do it as postgres user
			alter role chembl in database chembl set search_path to 'chembl33';

	==Installing dependent packages==		==Installing dependent packages==

2020-11-09T16:56:16Z

← Older revision		Revision as of 16:56, 9 November 2020
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	Here is the tutorial for building a ChEMBL for SEA based from Matt O'Meara's scripts		Here is the tutorial for building a ChEMBL for SEA based from Matt O'Meara's scripts
	Updated 11/06/2020 ~~by Khanh Tang~~
			Updated 11/06/2020

	==Setting up Postgres==		==Setting up Postgres==

2020-11-07T00:46:20Z

Loading ChEMBL on PHI server

← Older revision		Revision as of 00:46, 7 November 2020
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	==Loading ChEMBL on PHI server==		==Loading ChEMBL on PHI server==
	* Set up .pantry_config file in home directory		=== Set up .pantry_config file in home directory ===
	<div class="toccolours mw-collapsible mw-collapsed">		<div class="toccolours mw-collapsible mw-collapsed">
	'''Read more'''		'''Read more'''
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	</div>		</div>
	</div>		</div>
	* Loading ChEMBL into '''mem2''' server		=== Loading ChEMBL into '''mem2''' server ===
	This is recommend to have 2 terminal open: one for R and one open the R script. Execute code by chunks of code.		This is recommend to have 2 terminal open: one for R and one open the R script. Execute code by chunks of code.

2020-11-07T00:45:53Z

Loading ChEMBL on PHI server

← Older revision		Revision as of 00:45, 7 November 2020
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	"staging_directory" : "<setup_dir>/pantry_sets",		"staging_directory" : "<setup_dir>/pantry_sets",
	"login" : {		"login" : {
	"dbname" : "~~momeara~~",		"dbname" : "chembl",
	"host" : "~~phi.cluster.ucsf.bkslab.org~~",		"host" : "mem2",
	"user" : ~~<username>~~,		"user" : "chembl",
	"password" : ~~<password>~~,		"password" : "",
	"port" : ~~5432~~		"port" : 5433
	}		}
	}		}
	</div>		</div>
	</div>		</div>
	* Loading ChEMBL into '''~~phi~~''' server		* Loading ChEMBL into '''mem2''' server
	This is recommend to have 2 terminal open: one for R and one open the R script. Execute code by chunks of code.		This is recommend to have 2 terminal open: one for R and one open the R script. Execute code by chunks of code.

2020-11-07T00:13:07Z

← Older revision		Revision as of 00:13, 7 November 2020
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	Here is the tutorial for building a ChEMBL for SEA based from Matt O'Meara's scripts		Here is the tutorial for building a ChEMBL for SEA based from Matt O'Meara's scripts
			Updated 11/06/2020 by Khanh Tang

	==Setting up Postgres==		==Setting up Postgres==
	~~Updated 11/06/2020~~
	ChEMBL database is located on mem2 (postgres v12.3)		ChEMBL database is located on mem2 (postgres v12.3)
	psql -h mem2 -U chembl -d chembl -p 5433		psql -h mem2 -U chembl -d chembl -p 5433

	# basic psql commands you should know		# basic psql commands you should know
	- To list all tables: \dt		- To list all tables: \dt

2020-11-07T00:12:22Z

Setting up Postgres

← Older revision		Revision as of 00:12, 7 November 2020
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	==Setting up Postgres==		==Setting up Postgres==
	~~Login~~ (~~ask Chinzo or John for creating credential to login to phi server~~)		Updated 11/06/2020
	psql -h ~~phi.cluster.ucsf.bkslab.org~~ -U ~~momeara~~ -d ~~momeara~~ -p ~~5432~~		ChEMBL database is located on mem2 (postgres v12.3)
	~~yum install postgresql95~~-~~devel //check if this has already been installed in /usr~~		psql -h mem2 -U chembl -d chembl -p 5433
			# basic psql commands you should know
			- To list all tables: \dt
			- To list all users: \du
			- To list all schemas: \dn
			- To view table setup: \d+ <table_name>

	==Installing dependent packages==		==Installing dependent packages==

2019-10-11T17:41:41Z

← Older revision		Revision as of 17:41, 11 October 2019
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	Here is the tutorial for building a ChEMBL for SEA based on Matt O'Meara		Here is the tutorial for building a ChEMBL for SEA based from Matt O'Meara's scripts

	==Setting up Postgres==		==Setting up Postgres==

2019-10-11T17:40:58Z

Script 1: Get ZINC info for ChEMBL

← Older revision		Revision as of 17:40, 11 October 2019
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	'''Script 1-8 notes'''		'''Script 1-8 notes'''
	===Script 1: Get ZINC info for ChEMBL===		===Script 1: Get ZINC info for ChEMBL===
	*Specify ~~where to save ZINC data~~		*Specify tmp directory
	> write("TMP = YOUR_PATH_VARIABLE", file=file.path('~/.Renviron')) //on R console		> write("TMP = YOUR_PATH_VARIABLE", file=file.path('~/.Renviron')) //on R console

2019-10-11T17:39:49Z

Setting up Matt's R packages

← Older revision		Revision as of 17:39, 11 October 2019
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	yum install postgresql95-devel //check if this has already been installed in /usr		yum install postgresql95-devel //check if this has already been installed in /usr

	==~~Setting up Matt's R~~ packages==		==Installing dependent packages==
	~~Matt's R package that uses for process Postgres from R that has scripts for loading ChEMBL~~
	~~[https://github.com/momeara/BioChemPantry Link to git hub ]~~

	=== Install [http://github.com/momeara/BioChemPantry BioChemPantry]===		=== Install [http://github.com/momeara/BioChemPantry BioChemPantry]===
			R package written by Matt O'Meara for building ChEMBL library for SEA
	R		R
	install.packages("devtools")		install.packages("devtools")

2019-10-10T18:08:22Z

← Older revision		Revision as of 18:08, 10 October 2019
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	[[Category:SEA]][[Category:ChEMBL]] [[Category:Curator]]		[[Category:SEA]][[Category:ChEMBL]] [[Category:Curator]] [[Category:Khanh]]