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Fix remaining points by drpatelh

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Alexander Peltzer 2019-07-30 18:53:00 +02:00
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4
README.md
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@ -83,8 +83,8 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs
Currently documentation is available for the following clusters:
* [AQUILA](docs/aquila.md)
* [BINAC](docs/binac.md)
* [BIGPURPLE](docs/bigpurple.md)
* [BINAC](docs/binac.md)
* [CCGA](docs/ccga.md)
* [CCGA_DX](/docs/ccga_dx.md)
* [CFC](docs/binac.md)
@ -98,8 +98,8 @@ Currently documentation is available for the following clusters:
* [PRINCE](docs/prince.md)
* [SHH](docs/shh.md)
* [UCT_HEX](docs/uct_hex.md)
* [UPPMAX-DEVEL](docs/uppmax-devel.md)
* [UPPMAX](docs/uppmax.md)
* [UPPMAX-DEVEL](docs/uppmax-devel.md)
* [UZH](docs/uzh.md)
### Uploading to `nf-core/configs`

28
docs/pasteur.md
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@ -4,33 +4,35 @@ All nf-core pipelines have been successfully configured for use on the tars clus
To use, run the pipeline with `-profile pasteur`. This will download and launch the [`pasteur.config`](../conf/pasteur.config) which has been pre-configured with a setup suitable for the Pasteur cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
## Running the workflow on the Pasteur cluster
Nextflow is not installed by default on the Pasteur cluster.
- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command.
Nextflow shouldn't run directly on the submission node but on a compute node.
The compute nodes don't have access to internet so you need to run it offline.
To do that:
1. Create a virtualenv to install nf-core
```bash
module purge
module load Python/3.6.0
module load java
module load singularity
cd /path/to/nf-core/workflows
virtualenv .venv -p python3
. .venv/bin/activate
```
```bash
module purge
module load Python/3.6.0
module load java
module load singularity
cd /path/to/nf-core/workflows
virtualenv .venv -p python3
. .venv/bin/activate
```
2. Install nf-core: [here](https://nf-co.re/tools#installation)
3. Get nf-core pipeline and container: [here](https://nf-co.re/tools#downloading-pipelines-for-offline-use)
4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/rnaseq/blob/master/docs/usage.md#--custom_config_base)
4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/configs#offline-usage)
5. Run nextflow on a compute node:
```bash
# create a terminal
tmux

2
nfcore_custom.config
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@ -33,8 +33,8 @@ profiles {
prince { includeConfig "${params.custom_config_base}/conf/prince.config" }
shh { includeConfig "${params.custom_config_base}/conf/shh.config" }
uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" }
uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" }
uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" }
uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" }
}