Experiments Attachments For LPMX

This repository contains benchmark experiment scripts for LPMX.

To reproduce the experiments inside this repository, virtualbox and vagrant are needed.

Requirement

1. Vagrant https://www.vagrantup.com/
2. Oracle VM Virtualbox https://www.virtualbox.org/

To reproduce the composability experiment

open the terminal on your machine and type the following commands:

vagrant box add jasonyangshadow/composability
vagrant init jasonyangshadow/composability
vagrant up
vagrant ssh

Then you are in the virtual machine and all containers used in the experiment are configured and installed properly

A shell script named run.sh inside the home directory is used for the composability experiment, which has the very same content of the script named composability.sh inside this repository. Another script named composability_helper.sh is the real script executed inside the container for real genome analysis. Anyway, you do not need to download and put these scripts inside virtual machines, because they are also packaged and included inside the exported vagrant box.

To reproduce the benchmark experiment

open the terminal on your machine and type the following commands:

vagrant box add jasonyangshadow/benchmark_ubuntu1804
vagrant init jasonyangshadow/benchmark_ubuntu1804
vagrant up
vagrant ssh

Then you are in the virtual machine and all containers used in the experiment are configured and installed properly

A shell script named installation_benchmark.sh inside the home directory is used for the package installation performance benchmark test. It contains necessary bash commands for automating the experiment, just run it by the following command:

The time cost for installing packages is evaluated by the time command available in the Linux system.

cd ~ && ./installation_benchmark.sh

Another shell script named container_creation_benchmark.sh inside the home directory is used for the container creation benchmark test. It also contains necessary bash commands for automating the experiment.

To run the bash script:

cd ~ && ./container_creation_benchmark.sh

Also for a python script named image_convertion_benchmark.py, it is used for Docker image convertion benchmark test for Singularity and LPMX. It is also included inside the exported box.

Scripts inside sv folder

The scripts included inside the sv folder is the GATK SV call executed on HPC (shirokane supercomputer), these scripts could not directly run in your environment, but they can help you reproduce these experiments to some extends. The script named hg002_generate_data.py will help generate and download necessary HG002 reads and this data can be used for further analysis shown in sv scripts folder. LPMX and bare host use different commands to launch the analysis tools, so please be careful on the paths of data. Date used inside the experiment: GRCh38: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
HG002: file HG002_data_list

GPGPU Guppy basecaller experiment

The data used inside the GPGPU mode of Guppy basecaller is available from the file NA12878-IVT-RNA_All.files.txt

Raw experiment data file is experiment_data.xlsx

Notice:

All these experiment scripts are updated and available at https://github.com/JasonYangShadow/experiment_attachments, make sure receiving the latest version from the Github repository.