Unverified Commit 6fd6cf2f authored by Laurent Modolo's avatar Laurent Modolo
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README.md: mv getting started in a new file

parent 01dac1f9
......@@ -13,68 +13,7 @@ git pull upstream master
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 initialize a given tools run the following command:
```sh
src/docker_modules/<tool_name>/<tool_version>/docker_init.sh
```
For example to initialize `file_handle` version `0.1.1`, run:
```sh
src/docker_modules/file_handle/0.1.1/docker_init.sh
```
To initialize all the tools:
```sh
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
```sh
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:
```sh
src/nf_modules/<tool_name>/<tool_version>/tests.sh
```
For example to run the tests on `Bowtie2` run:
```sh
src/nf_modules/bowtie2/tests.sh
```
[you can follow them here.](doc/getting_started.md)
## Available tools
......
## 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 initialize a given tools run the following command:
```sh
src/docker_modules/<tool_name>/<tool_version>/docker_init.sh
```
For example to initialize `file_handle` version `0.1.1`, run:
```sh
src/docker_modules/file_handle/0.1.1/docker_init.sh
```
To initialize all the tools:
```sh
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
```sh
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:
```sh
src/nf_modules/<tool_name>/<tool_version>/tests.sh
```
For example to run the tests on `Bowtie2` run:
```sh
src/nf_modules/bowtie2/tests.sh
```
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