Build ChEMBL for SEA: Difference between revisions

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Login (ask Chinzo or Ben for creating credential to login to phi server)
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
   psql -h phi.cluster.ucsf.bkslab.org -U momeara -d momeara -p 5432
   yum install postgresql95-devel
   yum install postgresql95-devel //check if this has already install in /usr
==Setting up R BioChemPantry==
==Setting up R BioChemPantry==
Matt's R package that uses for process Postgres from R that has scripts for loading ChEMBL
Matt's R package that uses for process Postgres from R that has scripts for loading ChEMBL
[Link to git hub https://github.com/momeara/BioChemPantry]
[Link to git hub https://github.com/momeara/BioChemPantry]
* Download BioChemPantry
 
=== Download BioChemPantry ===
  R
  R
  install.packages("devtools")
  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")
  devtools::install_github("momeara/BioChemPantry")
* Set up library building script  
=== 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
  cd <dir>/BioChemPantry/vignette/sets
  cp chembl23 chembl25
  cp chembl23 chembl25
  cd chembl25/scripts
  cd chembl25/scripts
  replace string contains "chembl23" with "chembl25" in script 0-8
  replace string contains "chembl23" with "chembl25" in script 0-8
==Download Zr==
devtools::install_github("momeara/Zr")
==Loading ChEMBL for SEA==
==Loading ChEMBL for SEA==

Revision as of 19:15, 10 April 2019

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 R BioChemPantry

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

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