diff --git a/doc/TP_computational_biologists.md b/doc/TP_computational_biologists.md index baf148389f788570e95b1f6f31d837970280deda..f064e46c8d302257d28d1b3765ee298ec3e939a5 100644 --- a/doc/TP_computational_biologists.md +++ b/doc/TP_computational_biologists.md @@ -13,23 +13,23 @@ highlight: tango 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). +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 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 [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`. +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) are paired with a [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) file like following example for `Kallisto` version `0.43.1`: +[`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) are 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 ../ +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* +-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) @@ -48,14 +48,14 @@ 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/). +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`](./src/docker_modules/Kallisto/0.44.0/Dockerfile) is a succession of `bash` commands executed as the **root** user within the container. -When you build your [`Dockerfile`](./src/docker_modules/Kallisto/0.44.0/Dockerfile), instead of launching many time the [`docker_init.sh`](./src/docker_modules/Kallisto/0.44.0/docker_init.sh) script you can connect to a base container in interactive mode to launch tests your commands. +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 you can connect to a base container in interactive mode to launch tests your commands. ```sh docker run -it ubuntu:18.04 bash @@ -80,16 +80,16 @@ The last step to wrap your tool, is to make it available in nextflow. For this y 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/ +-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* +-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 intruction for two profiles : `sge` and `docker`.