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