From c13d38c799682865a1c39278757779437ee86d77 Mon Sep 17 00:00:00 2001
From: elabaron <emmanuel.labaronne@ens-lyon.fr>
Date: Thu, 12 Jul 2018 08:21:20 +0000
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+---
+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.
+
+You can read more on this process [here](https://guides.github.com/introduction/flow/)
+
--
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