mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-12-22 18:38:17 +00:00
38 lines
2.5 KiB
Markdown
38 lines
2.5 KiB
Markdown
# nf-core/configs: Computerome 2.0 Configuration
|
|
|
|
To use, run the pipeline with `-profile computerome`. This will download and launch the [`computerome.config`](../conf/computerome.config) which has been pre-configured with a setup suitable for the Computerome cluster.
|
|
|
|
## Using the Computerome config profile
|
|
|
|
Before running the pipeline you will need to load `Nextflow` using the environment module system (this can be done with e.g. `module load tools Nextflow/<VERSION>` where `VERSION` is e.g. `20.10`).
|
|
|
|
To use, run the pipeline with `-profile computerome` (one hyphen).
|
|
This will download and launch the [`computerome.config`](../conf/computerome.config) which has been pre-configured with a setup suitable for the Computerome servers.
|
|
It will enable `Nextflow` to manage the pipeline jobs via the `Torque` job scheduler.
|
|
Using this profile, `Singularity` image(s) containing required software(s) will be downloaded before execution of the pipeline.
|
|
|
|
Recent version of `Nextflow` also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images. The computerome configuration uses your project's scratch folder as the cachedir if not specified.
|
|
|
|
In addition to this config profile, you will also need to specify a Computerome project id.
|
|
You can do this with the `--project` flag (two hyphens) when launching `Nextflow`.
|
|
For example:
|
|
|
|
```bash
|
|
# Launch a nf-core pipeline with the computerome profile for the project id ab00002
|
|
$ nextflow run nf-core/<PIPELINE> -profile computerome --project ab00002 [...]
|
|
```
|
|
|
|
> NB: If you're not sure what your Computerome project ID is, try running `groups`.
|
|
|
|
Remember to use `-bg` to launch `Nextflow` in the background, so that the pipeline doesn't exit if you leave your terminal session.
|
|
Alternatively, you can also launch `Nextflow` in a `screen` or a `tmux` session.
|
|
|
|
## About Computerome 2.0
|
|
|
|
The Danish National Supercomputer for Life Sciences (a.k.a. Computerome) is installed at the DTU National Lifescience Center at Technical University of Denmark.
|
|
|
|
The computer hardware is funded with grants from Technical University of Denmark (DTU), University of Copenhagen (KU) and Danish e-infrastructure Cooperation (DeiC) - also, it is the official Danish ELIXIR Node.
|
|
|
|
Computerome 1.0 was opened in November 2014 at #121 on TOP500 Supercomputing Sites.
|
|
|
|
The current setup, Computerome 2.0, was opened in 2019. It's compute resources consists of 31760 CPU cores with 210 TeraBytes of memory, connected to 17 PetaBytes of High-performance storage,
|