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 === | |||
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:$PATH | |||
export LIBPQ_DIR=/usr/pgsql-9.5/ | |||
export LIBRARY_PATH=/usr/pgsql-9.5/lib | |||
devtools::install_github("momeara/BioChemPantry") | devtools::install_github("momeara/BioChemPantry") | ||
=== Download Zr === | |||
devtools::install_github("momeara/Zr") | |||
=== Download SEAR === | |||
require(devtools) | |||
install_version("data.table", version = "1.11.8", repos = "http://cran.us.r-project.org") | |||
devtools::install_github("momeara/SEAR") | |||
==Set up library building script== | |||
cd <dir>/BioChemPantry/vignette/sets | cd <dir>/BioChemPantry/vignette/sets | ||
cp chembl23 chembl25 | cp chembl23 chembl25 | ||
cd chembl25/scripts | cd chembl25/scripts | ||
replace string contains "chembl23" with "chembl25" in script 0-8 | replace string contains "chembl23" with "chembl25" in script 0-8 | ||
==Loading ChEMBL for SEA== | ==Loading ChEMBL for SEA== |
Revision as of 19:15, 10 April 2019
Here is the tutorial for building a ChEMBL for SEA based on Matt O'Meara
Setting up Postgres
Login (ask Chinzo or Ben for creating credential to login to phi server)
psql -h phi.cluster.ucsf.bkslab.org -U momeara -d momeara -p 5432 yum install postgresql95-devel //check if this has already install in /usr
Setting up R BioChemPantry
Matt's R package that uses for process Postgres from R that has scripts for loading ChEMBL [Link to git hub https://github.com/momeara/BioChemPantry]
Download BioChemPantry
R install.packages("devtools")
BioChemPantry is dependent on RPostgres package which required pgsql version > 9.0. Recommend using develop version of pgsql-9.5
//on bash export PATH=/usr/pgsql-9.5/bin:$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