diff --git a/doc/TP_experimental_biologists.md b/doc/TP_experimental_biologists.md index a0d4dfccd4844f2b05a29d78a716151f85d032a4..2b622187617db7db00872b9d60327294a3dd75e1 100644 --- a/doc/TP_experimental_biologists.md +++ b/doc/TP_experimental_biologists.md @@ -351,6 +351,43 @@ You can copy to your `src/RNASeq.nf` file the relevant content of [src/nf_module We are going to work with paired-end so only copy the relevant processes. The `index_fasta` process need to take as input the output of your `fasta_from_bed` process. The `fastq` input of your `mapping_fastq` process need to take as input the output of your `index_fasta` process and the `trimming` process. Commit your work and test your pipeline. +You now have a RNASeq analysis pipeline that can run locally with Docker ! +# Run your RNASeq pipeline on the PSMN +First you need to connect to the PSMN: +```sh +login@allo-psmn +login@e5-2667v4comp1 +``` + +## Set your environement + +Make the LBMC modules available to you: + +```sh +ln -s /Xnfs/lbmcdb/common/modules/modulefiles ~/privatemodules +echo "module use ~/privatemodules" >> .bashrc +``` + +Then you need to clone your pipeline and get the data : + +```sh +git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr/lmodolo/nextflow.git +cd nextflow/data +git clone -c http.sslVerify=false https://gitlab.biologie.ens-lyon.fr/LBMC/tiny_dataset.git +cd .. +``` + +## Run nextflow + +As we don't want nextflow to be killed in case of deconnection we start by launching `tmux`. In case of deconnection, you can restore your session with the command `tmux a`. + +```sh +tmux +module load nextflow/0.28.2 +nextflow src/RNASeq.nf -c src/RNASeq.config -profile sge --fastq "data/tiny_dataset/fastq/*_R{1,2}.fastq" --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" --bed "data/tiny_dataset/annot/tiny.bed" +``` + +You just ran your pipeline on the PSMN !