kstawiski/seq-pipeline

Workspace for data science projects and NGS pipelines. Contains RStudio, Jupyter Notebook, VSCode and file manager. Can connect to Tailscale network to bypass firewalls.

Welcome to seq-pipeline!

Workspace for data science projects and NGS pipelines by Konrad Stawiski. Contains everything you can imagine. Can connect to tailscale network to bypass firewalls. Also contains OmicSelector preinstalled.

Start to work:

This is the Docker image with VSCode, RStudio, Jupyter Notebook and file manager running. Great for development.

docker pull kstawiski/seq-pipeline
docker run --rm -d --name kgs24-work --hostname $(hostname)-work -v $(pwd):/work/ -v /home/$USER/:/home/$USER/ -p 26969:80 --privileged -v /var/run/docker.sock:/var/run/docker.sock kstawiski/seq-pipeline

Command above mounts your working directory as /work. Just go to http://localhost:26969 to start work or setup tunnel as below.

Note that when using Docker in Docker, for example by running the WDL pipeline via Cromwell, the path /work will not work. You can make a symlink on host device or bind the exact same path to the docker container.

Nvidia CUDA:

For NVIDIA CUDA support use kstawiski/seq-pipeline-gpu image:

docker pull kstawiski/seq-pipeline-gpu
docker run --rm -d --gpus all --name kgs24-work --hostname $(hostname)-work -v $(pwd):/work/ -p 26969:80 --privileged -v /home/$USER/:/home/$USER/ -v /var/run/docker.sock:/var/run/docker.sock kstawiski/seq-pipeline-gpu

Setup tunnel:

You need your free Tailscale network ID XXX, than run:

docker exec kgs24-work tailscale up --advertise-exit-node --accept-routes --authkey=XXX

Authkey setup - https://login.tailscale.com/admin/settings/keys

Alternatively, you can use ngrok, e.g. /ngrok http 8080 --log=stdout > /ngrok.log & (may require ngrok setup, ngrok is located in /ngrok).

Start new project:

Alternatively, you can set up directory for projects and operate using delivered pipelines and scripts:

git clone https://github.com/kstawiski/seq-pipeline.git .
./work.sh project_name

Pipelines

• Whole Exome Sequencing (tumor only somatic mutations) - TO DO

Tools used (credits)

• RStudio - https://www.rstudio.com/
• Jupyter Notebook - https://jupyter.org/
• VSCode - https://code.visualstudio.com/, https://github.com/coder/code-server
• Terminal is using https://github.com/butlerx/wetty
• Resources monitor uses https://github.com/DanielnetoDotCom/ServerMonitor
• Notes use https://github.com/artyuum/simple-note