getting_started.md

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

To run nextflow on you computer you need to have java (>= 1.8) installed.

java --version

To be able to easily test tools already implemented for nextflow on your computer (src/nf_modules/ to see their list). You need to have docker installed.

docker run hello-world

Installing

To install nextflow on you computer simply run the following command:

src/install_nextflow.sh

Then to initialize a given tools run the following command:

src/docker_modules/<tool_name>/<tool_version>/docker_init.sh

For example to initialize file_handle version 0.1.1, run:

src/docker_modules/file_handle/0.1.1/docker_init.sh

To initialize all the tools:

find src/docker_modules/ -name "docker_init.sh" | awk '{system($0)}'

Running the tests

To run tests we first need to get a training set

cd data
git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git
cp tiny_dataset/fastq/tiny_R1.fastq tiny_dataset/fastq/tiny2_R1.fastq
cp tiny_dataset/fastq/tiny_R2.fastq tiny_dataset/fastq/tiny2_R2.fastq
cp tiny_dataset/fastq/tiny_S.fastq tiny_dataset/fastq/tiny2_S.fastq
cd ..

Then to run the tests for a given tools run the following command:

src/nf_modules/<tool_name>/<tool_version>/tests.sh

For example to run the tests on Bowtie2 run:

src/nf_modules/bowtie2/tests.sh