Build ChEMBL for SEA: Difference between revisions
Jump to navigation
Jump to search
(Created page with "Here is the tutorial for building a ChEMBL for SEA based on Matt O'Meara ==Setting up Postgres== Login psql -h phi.cluster.ucsf.bkslab.org -U momeara -d momeara -p 5432") |
No edit summary |
||
Line 2: | Line 2: | ||
==Setting up Postgres== | ==Setting up Postgres== | ||
Login | 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 | |||
==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") | |||
devtools::install_github("momeara/BioChemPantry") | |||
* 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 | |||
==Download Zr== | |||
devtools::install_github("momeara/Zr") | |||
==Loading ChEMBL for SEA== |
Revision as of 22:29, 8 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
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") devtools::install_github("momeara/BioChemPantry")
- 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
Download Zr
devtools::install_github("momeara/Zr")