TP_computational_biologists.md

---
title: "TP for computational biologists"
author: Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr)
date: 20 Jun 2018
output:
pdf_document:
toc: true
toc_depth: 3
    number_sections: true
highlight: tango
    latex_engine: xelatex
---

The goal of this practical is to learn how to *wrap* tools in [Docker](https://www.docker.com/what-docker) or [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules) to make them available to nextflow on a personal computer or at the [PSMN](http://www.ens-lyon.fr/PSMN/doku.php).

Here we assume that you followed the [TP for experimental biologists](./TP_experimental_biologists.md), and that you know the basics of [Docker containers](https://www.docker.com/what-container) and [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules). We are also going to assume that you know how to build and use a nextflow pipeline from the template [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow).

For the practical you can either work with the WebIDE of Gitlab, or locally as described in the [git: basis formation](https://gitlab.biologie.ens-lyon.fr/formations/git_basis).

# Docker

To run a tool within a [Docker container](https://www.docker.com/what-container) you need to write a `Dockerfile`.

[`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) are found in the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) project under `src/docker_modules/`. Each [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) is paired with a [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) file like following the example for `Kallisto` version `0.43.1`:

```sh
$ ls -l src/docker_modules/Kallisto/0.43.1/
total 16K                                                                        
drwxr-xr-x 2 laurent users 4.0K Jun 5 19:06 ./                                  
drwxr-xr-x 3 laurent users 4.0K Jun 6 09:49 ../                                 
-rw-r--r-- 1 laurent users  587 Jun  5 19:06 Dockerfile                          
-rwxr-xr-x 1 laurent users 79 Jun 5 19:06 docker_init.sh*                     
```

## [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh)
The [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) is a simple sh script with executable rights (`chmod +x`). By executing this script, the user creates a [Docker container](https://www.docker.com/what-container) with the tool installed a specific version. You can check the [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) file of any implemented tools as a template.

Remember that the name of the [container](https://www.docker.com/what-container) must be in lower case and in the format `<tool_name>:<version>`.
For tools without a version number you can use a commit hash instead.

## [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile)

The recipe to wrap your tool in a [Docker container](https://www.docker.com/what-container) is written in a [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) file.

For `Kallisto` version `0.44.0` the header of the `Dockerfile` is :

```Docker
FROM ubuntu:18.04
MAINTAINER Laurent Modolo

ENV KALLISTO_VERSION=0.44.0
```

The `FROM` instruction means that the [container](https://www.docker.com/what-container) is initialized from a bare installation of Ubuntu 18.04. You can check the versions of Ubuntu available [here](https://hub.docker.com/_/ubuntu/) or others operating systems like [debian](https://hub.docker.com/_/debian/) or [worst](https://hub.docker.com/r/microsoft/windowsservercore/).

Then we declare the *maintainer* of the container. Before declaring an environment variable for the container named `KALLISTO_VERSION`, which contains the version of the tool wrapped. This this bash variable will be declared for the user root within the [container](https://www.docker.com/what-container).

You should always declare a variable `TOOLSNAME_VERSION` that contains the version number of commit number of the tools you wrap. In simple cases you just have to modify this line to create a new `Dockerfile` for another version of the tool.

The following lines of the [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) are a succession of `bash` commands executed as the **root** user within the container.
Each `RUN` block is run sequentially by `Docker`. If there is an error or modifications in a `RUN` block, only this block and the following `RUN` will be executed.

You can learn more about the building of Docker containers [here](https://docs.docker.com/engine/reference/builder/#usage).

When you build your [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile), instead of launching many times the [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) script to tests your [container](https://www.docker.com/what-container), you can connect to a base container in interactive mode to launch tests your commands.

```sh
docker run -it ubuntu:18.04 bash
KALLISTO_VERSION=0.44.0
```

# SGE / [PSMN](http://www.ens-lyon.fr/PSMN/doku.php)

To run easily tools on the [PSMN](http://www.ens-lyon.fr/PSMN/doku.php), you need to build your own [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules).

You can read the Contributing guide for the [PMSN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) project [here](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/CONTRIBUTING.md)

# Nextflow

The last step to wrap your tool is to make it available in nextflow. For this you need to create at least 4 files, like the following for Kallisto version `0.44.0`:

```sh
ls -lR src/nf_modules/Kallisto
src/nf_modules/Kallisto/:
total 12
-rw-r--r-- 1 laurent users 866 Jun 18 17:13 kallisto.config
-rw-r--r-- 1 laurent users 2711 Jun 18 17:13 kallisto.nf
drwxr-xr-x 2 laurent users 4096 Jun 18 17:14 tests/

src/nf_modules/Kallisto/tests:
total 16
-rw-r--r-- 1 laurent users 551 Jun 18 17:14 index.nf
-rw-r--r-- 1 laurent users 901 Jun 18 17:14 mapping_paired.nf
-rw-r--r-- 1 laurent users 1037 Jun 18 17:14 mapping_single.nf
-rwxr-xr-x 1 laurent users 627 Jun 18 17:14 tests.sh*
```

The [`kallisto.config`](./src/nf_modules/Kallisto/kallisto.config) file contains instructions for two profiles : `sge` and `docker`.
The [`kallisto.nf`](./src/nf_modules/Kallisto/kallisto.nf) file contains nextflow processes to use `Kallisto`.

The [`tests/tests.sh`](./src/nf_modules/Kallisto/tests/tests.sh) script (with executable rights), contains a series of nextflow calls on the other `.nf` files of the [`tests/`](./src/nf_modules/kallisto/tests/) folder. Those tests correspond to execution of the processes present in the [`kallisto.nf`](./src/nf_modules/Kallisto/kallisto.nf) file on the [LBMC/tiny_dataset](https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset) dataset with the `docker` profile. You can read the *Running the tests* section of the [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md).

## [`kallisto.config`](./src/nf_modules/Kallisto/kallisto.config)

The `.config` file defines the configuration to apply to your process conditionally to the value of the `-profile` option. You must define configuration for at least the `sge` and `docker` profile.

```Groovy
profiles {
  docker {
    docker.temp = 'auto'
    docker.enabled = true
    process {
    }
  }
  sge {
    process{
    }
  }
```

### `docker` profile

The `docker` profile starts by enabling docker for the whole pipeline. After that you only have to define the container name for each process:
For example, for `Kallisto` with the version `0.44.0`, we have:

```Groovy
process {
  $index_fasta {
    container = "kallisto:0.44.0"
  }
  $mapping_fastq {
    container = "kallisto:0.44.0"
  }
}
```

### `sge` profile

The `sge` profile defines for each process all the informations necessary to launch your process on a given queue with SGE at the [PSMN](http://www.ens-lyon.fr/PSMN/doku.php).
For example, for `Kallisto`, we have:

```Groovy
process{
  $index_fasta {
    beforeScript = "module purge; module load Kallisto/0.44.0"
    executor = "sge"
    cpus = 1
    memory = "5GB"
    time = "6h"
    queueSize = 1000
    pollInterval = '60sec'
    queue = 'h6-E5-2667v4deb128'
    penv = 'openmp8'
  }
  $mapping_fastq {
    beforeScript = "module purge; module load Kallisto/0.44.0"
    executor = "sge"
    cpus = 4
    memory = "5GB"
    time = "6h"
    queueSize = 1000
    pollInterval = '60sec'
    queue = 'h6-E5-2667v4deb128'
    penv = 'openmp8'
  }
}
```

The `beforeScript` variable is executed before the main script for the corresponding process.

## [`kallisto.nf`](./src/nf_modules/Kallisto/kallisto.nf)

The [`kallisto.nf`](./src/nf_modules/Kallisto/kallisto.nf) file contains examples of nextflow process that execute Kallisto.

- Each example must be usable as it is to be incorporated in a nextflow pipeline.
- You need to define, default value for the parameters passed to the process. 
- Input and output must be clearly defined.
- Your process should be usable as a starting process or a process retrieving the output of another process.

For more informations on processes and channels you can check the [nextflow documentation](https://www.nextflow.io/docs/latest/index.html).

## Making your wrapper available to the LBMC

To make your module available to the LBMC you must have a `tests.sh` script and one or many `docker_init.sh` scripts working without errors.
All the processes in your `.nf` must be covered by the tests.

After pushing your modifications on your forked repository, you can make a Merge Request to the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) **dev** branch. Where it will be tested and integrated to the **master** branch.