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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: Currently documentation is available for the following clusters:
* [AQUILA](docs/aquila.md) * [AQUILA](docs/aquila.md)
* [BINAC](docs/binac.md)
* [BIGPURPLE](docs/bigpurple.md) * [BIGPURPLE](docs/bigpurple.md)
* [BINAC](docs/binac.md)
* [CCGA](docs/ccga.md) * [CCGA](docs/ccga.md)
* [CCGA_DX](/docs/ccga_dx.md) * [CCGA_DX](/docs/ccga_dx.md)
* [CFC](docs/binac.md) * [CFC](docs/binac.md)
@ -98,8 +98,8 @@ Currently documentation is available for the following clusters:
* [PRINCE](docs/prince.md) * [PRINCE](docs/prince.md)
* [SHH](docs/shh.md) * [SHH](docs/shh.md)
* [UCT_HEX](docs/uct_hex.md) * [UCT_HEX](docs/uct_hex.md)
* [UPPMAX-DEVEL](docs/uppmax-devel.md)
* [UPPMAX](docs/uppmax.md) * [UPPMAX](docs/uppmax.md)
* [UPPMAX-DEVEL](docs/uppmax-devel.md)
* [UZH](docs/uzh.md) * [UZH](docs/uzh.md)
### Uploading to `nf-core/configs` ### 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. 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 ## Running the workflow on the Pasteur cluster
Nextflow is not installed by default 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 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. 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. The compute nodes don't have access to internet so you need to run it offline.
To do that: To do that:
1. Create a virtualenv to install nf-core 1. Create a virtualenv to install nf-core
```bash
module purge ```bash
module load Python/3.6.0 module purge
module load java module load Python/3.6.0
module load singularity module load java
cd /path/to/nf-core/workflows module load singularity
virtualenv .venv -p python3 cd /path/to/nf-core/workflows
. .venv/bin/activate virtualenv .venv -p python3
``` . .venv/bin/activate
```
2. Install nf-core: [here](https://nf-co.re/tools#installation) 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) 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: 5. Run nextflow on a compute node:
```bash ```bash
# create a terminal # create a terminal
tmux tmux

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