gsClustBrowse

Shiny app for browsing the exported intensities from Genome Studio

Contains an R Markdown for the setup of the SQLite database that is the data store for the app to query.

There is also a R script in scripts that demonstrates how to access and query the database from within R

Installing pre-requisites

Mac OS

If you don't have homebrew install it by following the instructions at https://brew.sh, it will let you follow the next steps.

Database Drivers

You need to install the unixodbc drivers for PostgreSQL. This can be done through homebrew brew install psqlodbc.

Then you need to fill in the driver details in this file /usr/local/etc/odbcinst.ini as such:

[PostgreSQL UNICODE]
Description=PostgreSQL ODBC driver (Unicode version)
Driver=/usr/local/Cellar/psqlodbc/12.01.0000/lib/psqlodbcw.so
Debug=0
CommLog=1
UsageCount=1

N.B. the version number might differ so check the file exists first using ls /usr/local/Cellar/psqlodbc/12.01.0000/lib/psqlodbcw.so

Reference websites:

https://www.labkey.org/Documentation/wiki-page.view?name=odbcmac

https://db.rstudio.com/getting-started/connect-to-database/

Download/clone the repo

Download/clone the repo locally.

R libraries

install.packages('shiny')
install.packages('DT')
install.packages('tidyverse')
install.packages('dbplyr')
install.packages('DBI')
install.packages('odbc')
install.packages('config')
install.packages('shinythemes')
install.packages('ggrepel')
install.packages('RColorBrewer')

Create a config file

In the project/repo root you will need a file called config.yml which is used to supply the database connection information.

It should look like the following:

default:
  psql_ro:
    driver: 'PostgreSQL UNICODE'
    database: '<database_name>'
    server: '<server_address>'
    port: <port_number>
    user: '<db_username>'
    password: '<db_password>'

It is important this file doesn't get added to the repo

Ask Murray for the details