@@ -50,7 +50,40 @@ Note that the content of these two folders should never be saved on git.
The [doc](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/doc) folder contains the documentation of this practical course.
And most interestingly for you, the [src](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/src) contains code to wrapp tools. This folder contains two subdirectory. A `nf_modules` and a `sge_modules` folder.
And most interestingly for you, the [src](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tree/master/src) contains code to wrapp tools. This folder contains two subdirectory. A `docker_modules`, an `nf_modules` and an `sge_modules` folder.
### `docker_modules`
The `src/docker_modules` contains the code to wrapp tools in [Docker](https://www.docker.com/what-docker). [Docker](https://www.docker.com/what-docker) is a framework that allow you to execute software withing [containers](https://www.docker.com/what-container). The `docker_modules` contains directory corresponding to tools and subdirectories corresponding to their version.
```sh
ls-l src/docker_modules/
rwxr-xr-x 3 laurent _lpoperator 96 May 25 15:42 BEDtools/
drwxr-xr-x 4 laurent _lpoperator 128 Jun 5 16:14 Bowtie2/
drwxr-xr-x 3 laurent _lpoperator 96 May 25 15:42 FastQC/
drwxr-xr-x 4 laurent _lpoperator 128 Jun 5 16:14 HTSeq/
```
To each `tools/version` corresponds two files:
```sh
ls-l src/docker_modules/Bowtie2/2.3.4.1/
-rw-r--r-- 1 laurent _lpoperator 283 Jun 5 15:07 Dockerfile
-rwxr-xr-x 1 laurent _lpoperator 79 Jun 5 16:18 docker_init.sh*
```
The `Dockerfile` is the [Docker](https://www.docker.com/what-docker) recepi to create a [container](https://www.docker.com/what-container) containing `Bowtie2` in it's `2.3.4.1` version. And the `docker_init.sh` file is a small script to create the [container](https://www.docker.com/what-container) from this recipe.
By running this script you will be able to easily install tools in different version on your personnal computer and use it in your pipeline. Some of the advantages are:
- Whatever the computer, the installation and the results will be the same
- You can keep [container](https://www.docker.com/what-container) for old version of tools and run it on new systems (science = reproducibility)
- You don't have to bother with detious installation procedure, somebody else already did the job and wrote a `Dockerfile`.
- You can easly keep [container](https://www.docker.com/what-container) for differents version of the sam tools.
