genomics-invoicing

This is a project intended to automate the generation of genomic invoices to customers.

For future developers

Windows users

1. Setting up Windows Subsystem for Linux (WSL)

There are plenty of tutorials online, won't go into details here. Remember your WSL username and password, you will need it later.

2. Install R

The author of this entry uses Debian distribution of WSL, the installation process may be different depending on your WSL distro. See more here

To ensure we are using the same R version as the server, we would need to install an older version of R: 4.4.1. Run this command to start a text file to tell your system where to find this version:

sudo nano /etc/apt/sources.list.d/cran-r.list

In the window that pops up, put in the following command. Note: this is for Debian Bookworm ONLY!

deb http://cloud.r-project.org/bin/linux/debian bookworm-cran40/

Now type crtl-O to write the line and crtl-X to exit.

Next, run this to get identification for the download:

gpg --keyserver keyserver.ubuntu.com \
    --recv-key '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7'

And this command to add the identificatino to your system's recognised id:

gpg --armor --export '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7' | \
    sudo tee /etc/apt/trusted.gpg.d/cran_debian_key.asc

Now you are set with the repository. Check the validity of the repository with:

sudo apt-get update
apt-cache policy r-base

If you see "4.4.1-1~bookwormcran.0" in "candidates", you are all set. Now install R 4.4.1 with:

sudo apt-get install r-base=4.4.1-1~bookwormcran.0

Finally check installation with:

R --version

3. Install R studio server

Now install the latest R studio desktop. Go to the official R-studio site. IMPORTANT: Select your distro and version correctly. Follow step 3. Code is not shown here because the download link may change upon updates.

4. Launch dev space

Run this command in your bash shell

sudo rstudio-server start

if you see some text starting with "TTY detected.", you are good to go. Now open your browser and type in:

http://localhost:8787

you should see a window asking for a user name and password. Use your WSL username and password. Then you can see your development environment in your browser successfully deployed.

MAC users

to be filled

WEHI-RCPStudentInternship/genomics-invoicing