This repository contains the benchmarks for these pipelines:
To reproduce the figures from raw data clone this repository:
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-figures.sh
(if you don't want or cannot use Docker, it will be required to download and install the required dependencies: R, Datamash, Make and Groovy. See the included Dockefile for configuration details).
It will create the following files:
./rnaseq-toy/table.txt
./rnaseq-toy/fig_correlation.png
./nmdp-flow/table.txt
./nmdp-flow/fig_correlation.png
./piper-nf/table.txt
./piper-nf/fig_correlation.png
Benchmarks scripts and data are organised in separated folder depending the pipeline executed:
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 1fig_correlation.png
: the figure in included in the manuscript.
See the respective Makefile
s for more details.
Pipeline executions can be replicated following the instructions in the respective repositories, shown below: