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npg_basespace-smalt contains Dockerfiles for setting up smalt alignment pipelines inside a Docker container, that can be uploaded as a Illumina Basespace Native App.

Dockerfile builds everything from scratch.
Dockerfile.baseimage uses build-baseimage (see ../autobuild/baseimage) to avoid redundancy. This image will be uploaded to the Docker repository at one point.

Quick Start Instructions: Get it running on BaseSpace
  1. Create Dev Account
  2. Create Native App
  3. (For local testing): Install the SpaceDock VM
  4. Build image and push it to Basespace

    Use your BaseSpace credentials when prompted for username, password, and email

    sudo docker login

Build Image from Dockerfile

sudo docker build -t[yourRepoName]/smaltAligner .

Push Image to BaseSapce

sudo docker push[yourRepoName]/smaltAligner

  1. Copy and paste basespace/Input_Form.txt and basespace/Callback_js.txt into the Form Builder. Adjust image name in callback.js accordingly.
  2. In the Form Builder Preview find the sudo spacedock -a … command on the bottom right. SSH into SpaceDock VM and run that command.
  3. Select desired input samples, reference and output. Run the alignment with Send To Local Agent.
  4. Copy and paste basespace/Output_Report to Reports Builder.
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