Once ingredients have been procured, they are shelved in the pantry ready for use.

Bioinformatics datasets are provided by a wide range of groups, in a wide range formats, and are rapidly changing. This is an opinionated guide to collect and curate data sets. It sets up a local database of datasets that can be used for an integrated analysis.

to install:

1. Install a postgres database (http://www.postgresql.org/)

For example, to install postgres on a mac using Homebrew

brew install postgresql

then start the database with

brew services start postgresql

Setup up the database

psql postgres
# now in the psql prompt

CREATE ROLE pantry WITH LOGIN PASSWORD ‘password’;
CREATE DATABASE pantry;
GRANT CREATE ON DATABASE pantry TO pantry;

Enable password-free login (see (documentation](https://tableplus.com/blog/2019/09/how-to-use-pgpass-in-postgresql.html))

 echo "<host>:<port>:<dbname>:<user>:<password>" >> ${HOME}/.pgpass
 # where the values in <> are specific for your setup
 sudo chmod 600 ~/.pgpass
 echo "export PGPASSFILE=\'${HOME}.pgpass\'" >> ${HOME}/.zshrc

1a. Create the json file ~/.pantry_config that will be passed to dplyr::src_postgres to login to the database. For example:

{
  "staging_directory" : "/Users/maom/opt/pantry_sets",
  "login" : {
    "dbname" : "<database name>",
    "host" : "<host>",
    "user" : "<user>",
    "port" : <port>
  }
}

2. Install the package in R

install.packages("remotes")
remotes::install_github("momeara/BioChemPantry")

usage:

1. Install datasets

library(BioChemPantry)

2. Load datasets by following the vignettes in vignettes/sets/

3. Use datasets

library(plyr)
library(dplyr)
library(BioChemPantry)
pantry <- get_pantry(schema=<dataset>)

tbl <- pantry |> schema_tbl("<tbl>")