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update docs

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MaxUlysse 2019-12-05 15:18:01 +01:00
parent f41d325873
commit 99afe86ea9
2 changed files with 23 additions and 19 deletions
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8
conf/uppmax.config
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@ -27,10 +27,6 @@ params {
def hostname = "hostname".execute().text.trim() def hostname = "hostname".execute().text.trim()
if (hostname ==~ "r.*") {
params.max_cpus = 20
}
if (hostname ==~ "b.*") { if (hostname ==~ "b.*") {
params.max_memory = 109.GB params.max_memory = 109.GB
} }
@ -39,6 +35,10 @@ if (hostname ==~ "i.*") {
params.max_memory = 250.GB params.max_memory = 250.GB
} }
if (hostname ==~ "r.*") {
params.max_cpus = 20
}
profiles { profiles {
devel { devel {
params { params {

34
docs/uppmax.md
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@ -4,7 +4,9 @@ All nf-core pipelines have been successfully configured for use on the Swedish U
## Using the UPPMAX config profile ## Using the UPPMAX config profile
To use, run the pipeline with `-profile uppmax` (one hyphen). This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers. 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 uppmax` (one hyphen).
This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers.
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.
In addition to this config profile, you will also need to specify an UPPMAX project id. In addition to this config profile, you will also need to specify an UPPMAX project id.
You can do this with the `--project` flag (two hyphens) when launching nextflow. For example: You can do this with the `--project` flag (two hyphens) when launching nextflow. For example:
@ -23,18 +25,6 @@ Just run Nextflow on a login node and it will handle everything else.
A local copy of the iGenomes resource has been made available on all UPPMAX clusters so you should be able to run the pipeline against any reference available in the `igenomes.config`. A local copy of the iGenomes resource has been made available on all UPPMAX clusters so you should be able to run the pipeline against any reference available in the `igenomes.config`.
You can do this by simply using the `--genome <GENOME_ID>` parameter. You can do this by simply using the `--genome <GENOME_ID>` parameter.
## Running offline with Bianca
If running on Bianca, you will have no internet connection and these configs will not be loaded.
Please use the nf-core helper tool on a different system to download the required pipeline files, and transfer them to bianca.
This helper tool bundles the config files in this repo together with the pipeline files, so the profile will still be available.
Note that Bianca only allocates 7 GB memory per core so the max memory needs to be limited:
```bash
--max_memory "112GB"
```
## Getting more memory ## Getting more memory
If your nf-core pipeline run is running out of memory, you can run on a fat node with more memory using the following nextflow flags: If your nf-core pipeline run is running out of memory, you can run on a fat node with more memory using the following nextflow flags:
@ -50,9 +40,23 @@ Note that each job will still start with the same request as normal, but restart
All jobs will be submitted to fat nodes using this method, so it's only for use in extreme circumstances. All jobs will be submitted to fat nodes using this method, so it's only for use in extreme circumstances.
## devel config ## How to specify a UPPMAX cluster
If doing pipeline development work on Uppmax, this profile allows for faster testing. You actually do not need to, based on `hostnames`, configuration will be automatically applied for the cluster you are on following these specifications:
* `bianca`
* cpus available: 16 cpus
* memory available: 109 GB
* `irma`
* cpus available: 16 cpus
* memory available: 250 GB
* `rackham`
* cpus available: 20 cpus
* memory available: 125 GB
## Development config
If doing pipeline development work on UPPMAX, the `devel` profile allows for faster testing.
Applied after main UPPMAX config, it overwrites certain parts of the config and submits jobs to the `devcore` queue, which has much faster queue times. Applied after main UPPMAX config, it overwrites certain parts of the config and submits jobs to the `devcore` queue, which has much faster queue times.