getting_started.md

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. You can follow the building your pipeline guide to learn how to build your own pipelines.

Prerequisites

To run nextflow on your computer you need to have java (>= 1.8) installed.

java --version

and git

git --version

To be able to run existing tools in nextflow on your computer (src/nf_modules/ to see the list). You need to have docker installed.

docker run hello-world

Alternatively if you are on Linux, you can use singularity:

singularity run docker://hello-world

Installing

To install nextflow on your computer simply run the following command:

git clone git@gitbio.ens-lyon.fr:LBMC/nextflow.git
cd nextflow/
src/install_nextflow.sh

Running a toy RNASeq quantification pipeline

To run tests we first need to get a training set

cd data
git clone https://gitbio.ens-lyon.fr/LBMC/Hub/tiny_dataset.git
cp tiny_dataset/fastq/tiny_R1.fastq tiny_dataset/fastq/tiny2_R1.fastq
cp tiny_dataset/fastq/tiny_R2.fastq tiny_dataset/fastq/tiny2_R2.fastq
cp tiny_dataset/fastq/tiny_S.fastq tiny_dataset/fastq/tiny2_S.fastq
cd ..

Then to run the tests for a given tools run the following command:

./nextflow src/solution_RNASeq.nf --fastq "data/tiny_dataset/fastq/tiny2_R{1,2}.fastq.gz" --fasta "data/tiny_dataset/fasta/tiny_v2_10.fasta" --bed "data/tiny_dataset/annot/tiny.bed" -profile docker

Nextflow profile

By default le src/nextflow.config file define 4 different profiles

• -profile docker each process of the pipeline will be executed within a docker container locally
• -profile singularity each process of the pipeline will be executed within a singularity container locally
• -profile psmn each process will be sent as a separate job within a charliecloud container on the PSMN
• -profile ccin2p3 each process will be sent as a separate job within a singularity container on the CCIN2P3

If the containers are not found locally, they are automatically downloaded before running the process. For the PSMN and CCIN2P3, the singularity images are downloaded in a shared folder (/scratch/Bio/charliecloud for the PSMN, and /sps/lbmc/common/singularity/ for the CCIN2P3)

PSMN

To have access to charliecloud on the PSMN you need to add the followin path to your PATH variable:

PATH=/Xnfs/abc/charliecloud_bin/:$PATH
```

You can add this line in your `~/.bashrc` or `~/.zshrc` file

When running `nextflow` on the PSMN, we recommend to use `tmux` before launching the pipeline:


```sh
tmux
./nextflow src/solution_RNASeq.nf --fastq "data/tiny_dataset/fastq/tiny2_R{1,2}.fastq.gz" --fasta "data/tiny_dataset/fasta/tiny_v2_10.fasta" --bed "data/tiny_dataset/annot/tiny.bed" -profile psmn
```

Therefore, the `nextflow` process will continue to run even if you are disconnected.
You can re-attach the `tmux` session, with the command `tmux a` (and press `ctrl` `+` `b` `+` `d` to detach the attached session).

### CCIN2P3

When runnning `nextflow` on the CCIN2P3, you cannot use `tmux`, instead you should send a _daemon_ jobs which will launch the `nextflow` command.
You can edit the `src/ccin2p3.pbs` file to personalize your `nextflow` command and send it with the command:

```sh
qsub src/ccin2p3.pbs
```