Verified Commit 98db0358 authored by Laurent Modolo's avatar Laurent Modolo
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TP.md: PSMN section

parent 0dba9f2b
......@@ -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 !
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