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

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kstawiski/seq-pipeline

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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.

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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)

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

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