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Fix binac resources

This commit is contained in:
Alexander Peltzer 2019-10-28 13:22:12 +01:00
commit eb6d23254d
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8 changed files with 34 additions and 40 deletions

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@ -20,7 +20,7 @@ params {
igenomes_base = '/nfsmounts/igenomes'
max_memory = 1000.GB
max_cpus = 28
max_time = 168.h
max_time = 48.h
}
weblog{

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@ -8,25 +8,16 @@ params {
process {
executor = 'slurm'
module = 'singularity/3.2.1'
queue = 'c'
queue = { task.memory <= 170.GB ? 'c' : 'm' }
clusterOptions = { task.time <= 8.h ? '--qos short': task.time <= 48.h ? '--qos medium' : '--qos long' }
}
singularity.enabled = true
params {
target_qos = 'medium'
params.max_cpus = 36
params.max_memory = 170.GB
igenomesIgnore = true
}
if (params.target_qos == 'short') {
params.max_time = 8.h
process.clusterOptions = '--qos short'
} else if (params.target_qos == 'medium') {
params.max_time = 2.d
process.clusterOptions = '--qos medium'
} else {
params.max_time = 14.d
process.clusterOptions = '--qos long'
}
params.max_cpus = 36
params.max_memory = 4.TB
igenomes_ignore = true
igenomesIgnore = true //deprecated
}

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@ -55,7 +55,8 @@ params {
awsregion = "us-west-2"
awsqueue = "nextflow"
igenomesIgnore = true
igenomes_ignore = true
igenomesIgnore = true //deprecated
fc_extra_attributes = 'gene_name'
fc_group_features = 'gene_id'

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@ -16,7 +16,8 @@ process {
}
params {
igenomesIgnore = true
igenomes_ignore = true
igenomesIgnore = true //deprecated
max_memory = 750.GB
max_cpus = 80
max_time = 336.h

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@ -18,7 +18,8 @@ process {
}
params {
igenomesIgnore = true
igenomes_ignore = true
igenomesIgnore = true //deprecated
saveReference = true
max_memory = 64.GB
max_cpus = 20

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@ -19,5 +19,6 @@ params {
max_cpus = 32
max_memory = 128.GB
max_time = 192.h
igenomesIgnore = true
igenomes_ignore = true
igenomesIgnore = true //deprecated
}

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@ -16,7 +16,8 @@ process {
}
params {
igenomesIgnore = true
igenomes_ignore = true
igenomesIgnore = true //deprecated
max_memory = 256.GB
max_cpus = 28
max_time = 24.h

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@ -4,38 +4,36 @@ 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#)
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/configs#offline-usage)
5. Run nextflow on a compute node:
4. Get the nf-core Pasteur profile: [here](https://github.com/nf-core/rnaseq/blob/master/docs/usage.md#--custom_config_base)
5. Run nextflow on a compute node:
```bash
# create a terminal
tmux
tmux
# Get a compute node
salloc
@ -48,7 +46,7 @@ module load singularity
# Run nextflow workflow
nextflow run \\
/path/to/pipeline-dir/from/step/3/workflow \\
-resume
-resume
-profile pasteur \\
-with-singularity /path/to/pipeline-dir/from/step/3/singularity-images/singularity.img \\
--email my-email@pasteur.fr \\