From 082ba1ec232561fbbed95c2b602b8ef1393a8f6f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 31 May 2018 15:48:45 +0200
Subject: [PATCH] README.md : add installation guide

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 README.md | 80 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 80 insertions(+)

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+# nextflow pipeline
+
+This repository is a template and a library repository to help you build nextflow pipeline.
+
+## 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.
+
+```sh
+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.
+
+```sh
+docker run hello-world
+```
+
+### Installing
+
+To install nextflow on you computer simply run the following command:
+
+```sh
+src/install_nextflow.sh
+```
+
+Then to initialise a given tools run the following command:
+
+```sh
+src/nf_modules/<tool_name>/<tool_version>/docker_init.sh
+```
+
+for example to initialise `file_handle` version `0.1.1`, run:
+
+```sh
+src/nf_modules/file_handle/0.1.1/docker_init.sh
+```
+
+## Running the tests
+
+Explain how to run the automated tests for this system
+
+### Break down into end to end tests
+
+Explain what these tests test and why
+
+```
+Give an example
+```
+
+### And coding style tests
+
+Explain what these tests test and why
+
+```
+Give an example
+```
+
+## Contributing
+
+Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduct, and the process for submitting pull requests to us.
+
+## Versioning
+
+We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tags). 
+
+## Authors
+
+* **Laurent Modolo** - *Initial work*
+
+See also the list of [contributors](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/graphs/master) who participated in this project.
+
+## License
+
+This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) file for details
+
-- 
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