cbcrg/docker-benchmarks

Name: docker-benchmarks

Owner: Notredame Lab

Description: A benchmarks of genomic pipelines running in Docker containers

Created: 2015-05-14 17:13:07.0

Updated: 2017-02-27 09:24:46.0

Pushed: 2015-09-03 16:06:46.0

Homepage:

Size: 4613

Language: HTML

GitHub Committers

User	Most Recent Commit	# Commits
Paolo Di Tommaso	2015-09-03 16:06:42.0	34
Emilio Palumbo	2015-08-27 10:06:59.0	1
Pablo Prieto	2015-07-07 12:57:53.0	3

Other Committers

User	Email	Most Recent Commit	# Commits

README

Docker benchmarks

This repository contains the benchmarks for these pipelines:

• Rnaseq-toy
• Nmdp-flow
• Piper-nf

Quick start

To reproduce the figures from raw data clone this repository:

git clone https://github.com/cbcrg/docker-benchmarks.git && cd docker-benchmarks

Then pull the required Docker image:

docker pull cbcrg/make-peerj5515

Finally launch the make script using the following command:

docker run -v $PWD:$PWD -w $PWD cbcrg/make-peerj5515 bash make-all.sh

(if you don't want or cannot use Docker, you will need to download and install the required dependencies: R, Datamash, Make and Groovy. See the included Dockefile for configuration details).

Structure of the repository

Benchmarks scripts and data are organised in separate folders depending the pipeline executed:

• Rnaseq-toy
• nmdp-flow
• piper-nf

Each of these folders contains a Makefile and other scripts used by it to generate the figures. Raw data of each executions are the files docker_{1..10}/trace.csv and native_{1..10}/trace.csv in the same folder.

The main files produced by the make process are:

• table.txt: the numbers included in the Table 1
• fig_correlation.png: the figure in included in the manuscript.

See the respective Makefiles for more details.

Replicate benchmarks

Pipeline executions can be replicated following the instructions in the respective repositories, listed below:

• nmdp-flow
• piper-nf
• rnaseq-toy