diff --git a/doc/TP_experimental_biologists.md b/doc/TP_experimental_biologists.md index 44592213c258236b8589ebeec06a1ef4586c7019..0275d1997145aee88fae15beb486b0e9c5e308c9 100644 --- a/doc/TP_experimental_biologists.md +++ b/doc/TP_experimental_biologists.md @@ -72,30 +72,58 @@ ls -l src/docker_modules/Bowtie2/2.3.4.1/ -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. +The `Dockerfile` is the [Docker](https://www.docker.com/what-docker) recipe 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: +By running this script you will be able to easily install tools in different version on your personal 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. +- You don't have to bother with tedious installation procedure, somebody else already did the job and wrote a `Dockerfile`. +- You can easily keep [container](https://www.docker.com/what-container) for different version of the same tools. ### `sge_modules` -The `src/sge_modules` folder is not realy there. It's a submodule of the project [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules). To populate it locally you can use the following command: +The `src/sge_modules` folder is not really there. It's a submodule of the project [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules). To populate it locally you can use the following command: ```sh git submodule init ``` -Like for the `src/docker_modules` the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) project describe recepies to install tools and use them. The main difference is that you cannot use [Docker](https://www.docker.com/what-docker) on the PSMN. Instead you have to use another framework [Environement Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules) which allows you to load modules for specific tools and version. +Like for the `src/docker_modules` the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) project describe recipes to install tools and use them. The main difference is that you cannot use [Docker](https://www.docker.com/what-docker) on the PSMN. Instead you have to use another framework [Environment Module](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:modules) which allows you to load modules for specific tools and version. The [README.md](https://gitlab.biologie.ens-lyon.fr/PSMN/modules/blob/master/README.md) file of the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) respository contains all the instruction to be able to load the modules maintained by the LBMC en present in the [PSMN/modules](https://gitlab.biologie.ens-lyon.fr/PSMN/modules) respository. ### `nf_modules` The `src/nf_modules` folder contains templates of [nextflow](https://www.nextflow.io/) wrapper for the tools available in [Docker](https://www.docker.com/what-docker) and [SGE](http://www.ens-lyon.fr/PSMN/doku.php?id=documentation:tools:sge). The details of the [nextflow](https://www.nextflow.io/) wrapper will be presented in the next section. Alongside the `.nf` and `.config` there is a `tests` folder that contains a `tests.sh` script to run test on the tool. +# Build your own RNASeq pipeline + +In this section you are going to build your own pipeline for RNASeq analysis from the code available in the `src/nf_modules` folder. + +## Nextflow pipeline + +A pipeline is a succession of **process**. Each process has data input(s) and optional data output(s). Data flow are modeled as **channels**. + + +# Run your pipeline locally + +```sh +git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr/<usr_name>/nextflow.git +cd nextflow +src/install_nextflow.sh +``` + +## Create your Docker containers + +For this practical, we are going to need the following tools : + +- For Illumina adaptor removal : cutadapt +- For reads trimming by quality : UrQt +- For mapping and quantifying reads : Kallisto, RSEM and Bowtie2 + +To initialize these tools, follow the **Installing** section of the [README.md](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/blob/master/README.md) file. + +