Build ChEMBL for SEA

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Here is the tutorial for building a ChEMBL for SEA based on Matt O'Meara

Setting up Postgres

Login (ask Chinzo or Ben for creating credential to login to phi server)

 psql -h phi.cluster.ucsf.bkslab.org -U momeara -d momeara -p 5432
 yum install postgresql95-devel //check if this has already install in /usr

Setting up Matt's R packages

Matt's R package that uses for process Postgres from R that has scripts for loading ChEMBL Link to git hub

Download BioChemPantry

R
install.packages("devtools")

BioChemPantry is dependent on RPostgres package which required pgsql version > 9.0. Recommend using develop version of pgsql-9.5

//on bash
export PATH=/usr/pgsql-9.5/bin:$PATH
export LIBPQ_DIR=/usr/pgsql-9.5/
export LIBRARY_PATH=/usr/pgsql-9.5/lib
devtools::install_github("momeara/BioChemPantry")

Download Zr

devtools::install_github("momeara/Zr")

Download SEAR

require(devtools)
install_version("data.table", version = "1.11.8", repos = "http://cran.us.r-project.org")
devtools::install_github("momeara/SEAR")

Set up library building script

cd <dir>/BioChemPantry/vignette/sets
cp chembl23 chembl25
cd chembl25/scripts
replace string contains "chembl23" with "chembl25" in script 0-8

Loading ChEMBL for SEA