diff --git a/doc/TP_computational_biologists.md b/doc/TP_computational_biologists.md new file mode 100644 index 0000000000000000000000000000000000000000..ec6dfc7a6d1734805f072065be7e3664c110f075 --- /dev/null +++ b/doc/TP_computational_biologists.md @@ -0,0 +1,99 @@ +--- +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 on [Docker containers](https://www.docker.com/what-container) and [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules) usage. We also are 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 [git : the basis formation](https://gitlab.biologie.ens-lyon.fr/formations/git_basis). + +# Docker + +To run a tools within a [Docker container](https://www.docker.com/what-container) you need to write a `Dockerfile`. + +`Dockerfile` are found in the [pipelines/nextflow](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow) project under `src/docker_modules/`. Each `Dockerfile` are paired with a `docker_init.sh` file like following 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` +The `docker_init.sh` is a simple sh script with the executable right (`chmod +x`).By executing this script, the user creates the [Docker container](https://www.docker.com/what-container) for the tools in a specific version. You can check the `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. + +## `Dockerfile` + +The recipe to wrap your tool in a [Docker container](https://www.docker.com/what-container) is written in a `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 +``` + +This means that we initialize the [container](https://www.docker.com/what-container) from a bare installation of Ubuntu 18.04. You can check the ubuntu available versions [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 a environment variable for the container named `KALLISTO_VERSION` which contains the version of the tools wrapped. This means that this bash variable will be declared 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. Therefore in simple case you just have to modify this line to create a new `Dockerfile` for another version of the tool. + +The following of the `Dockerfile` is a succession of `bash` commands executed as the **root** user within the container. +When you build your `Dockerfile`, instead of launching many time the `docker_init.sh` script 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 +``` + +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). + +# SGE + +To run easily tools on the PSMN, 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 of the [PMSN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) [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` file contains intruction for two profiles : `sge` and `docker`. +The `Kallisto.nf` file contains nextflow processes to use `Kallisto`. + +The `tests/tests.sh` script, contains a serie of calls nextflow on the other `.nf` files of the `tests/` folder. Those tests correspond to execution of the processes present in the `Kallisto.nf` file on the [LBMC/tiny_dataset](https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset) dataset. You can read the *Running the tests* section of the [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md). +