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
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@@ -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:
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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).
