Singuliarity Container for Hail

• This project is supported by Research University Network grant "Precision Cancer Medicine"
• Integrative Database & Analytics Platform for Cancer Precision Medicine
• Maintain by: Bhoom Suktitipat, MD, PhD

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Overview

Singularity Container for Hail (hail.is)

1. built from Spark2.2.2, Anaconda3, and Hail v.0.2
2. Please download these three required component before start building. Save the files to hailSrc directory.

../hailSrc/Anaconda3-5.2.0-Linux-x86_64.sh
../hailSrc/spark-2.2.2-bin-hadoop2.7.tgz
../hailSrc/Hail-devel-1f253167d53c-Spark-2.2.0.zip

3. clone the github to pwd using git clone https://github.com/hypotheses/singhail.git

Your folder structure might look like these

`pwd`
   |--hailSrc: {source code for the required programs}
   |
   |--hailsing: {Singularity singhail git}

4. Build the image image: In vagrant virtual machine build an image using this command sudo singularity build --writable singhail.img Singularity

Working with the singhail container

NOTE: --login option is required to load conda To use the container: and bind the data directory from host /turtle/RUN/vcf to the container

singularity shell -B /turtle/RUN/vcf singhail.img --login

To modify the image start the container with --writable option

sudo singularity shell --writable singhail.img --login