diff --git a/doc/getting_started.md b/doc/getting_started.md index b1a01f13775b6e9c49726c713e53878189758040..e41ffe528fd9745322fec917e00ae407f1a5f389 100644 --- a/doc/getting_started.md +++ b/doc/getting_started.md @@ -42,6 +42,7 @@ src/install_nextflow.sh ## Running a toy RNASeq quantification pipeline To run tests we first need to get a training set + ```sh cd data git clone https://gitbio.ens-lyon.fr/LBMC/Hub/tiny_dataset.git @@ -63,16 +64,24 @@ 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 `singularity` container on the PSMN +- `-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/singularity` for the PSMN, and `/sps/lbmc/common/singularity/` for 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 @@ -83,10 +92,10 @@ You can re-attach the `tmux` session, with the command `tmux a` (and press `ctrl ### CCIN2P3 -When runnning `nextflow` on the CCIN2P3, you cannot use `tmux`, instead you should send a *daemon* jobs which will launch the `nextflow` command. +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 ``` - +````