From 8e4ddf6a4b5323ac07c9799cef52d6d075ff0518 Mon Sep 17 00:00:00 2001 From: Laurent Modolo <laurent.modolo@ens-lyon.fr> Date: Tue, 20 Apr 2021 12:13:59 +0200 Subject: [PATCH] getting_started.md: add ccin2p3 section --- doc/getting_started.md | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/doc/getting_started.md b/doc/getting_started.md index e480ff21..00e4e95f 100644 --- a/doc/getting_started.md +++ b/doc/getting_started.md @@ -1,6 +1,6 @@ # Getting Started -These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system. +These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. ## Prerequisites @@ -65,7 +65,10 @@ By default le `src/nextflow.config` file define 4 different profiles - `-profile psmn` each process will be sent as a separate job within a `singularity` 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 befor running the process. For the PSMN and CCIN2P3, the `singularity` images are downloaded in a shared folder (`/scratch/Bio/singularity` for the PSMN) +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) + + +### PSMN When running `nextflow` on the PSMN, we recommend to use `tmux` before launching the pipeline: @@ -77,6 +80,15 @@ tmux 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 +``` + ## Building your pipeline You can follow the [building your pipeline guide](./doc/building_your_pipeline.md). -- GitLab