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Merge pull request #183 from abims-sbr/abims

Add ABiMS
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Maxime Garcia 2020-10-23 09:57:20 +02:00 committed by GitHub
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@ -16,7 +16,7 @@ jobs:
needs: test_all_profiles
strategy:
matrix:
profile: ['awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'kraken', 'mpcdf', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'kraken', 'mpcdf', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
steps:
- uses: actions/checkout@v1
- name: Install Nextflow

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@ -94,6 +94,7 @@ See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs
Currently documentation is available for the following systems:
* [ABIMS](docs/abims.md)
* [AWSBATCH](docs/awsbatch.md)
* [BIGPURPLE](docs/bigpurple.md)
* [BI](docs/bi.md)

24
conf/abims.config Normal file
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@ -0,0 +1,24 @@
//Profile config names for nf-core/configs
params {
config_profile_description = 'The ABiMS cluster profile'
config_profile_contact = 'Gildas Le Corguillé (@lecorguille)'
config_profile_url = 'https://abims.sb-roscoff.fr'
}
singularity {
enabled = true
autoMounts = false
runOptions = '-B /scratch:/scratch -B /scratch2:/scratch2 -B /shared:/shared'
}
process {
executor = 'slurm'
}
params {
igenomes_ignore = true
igenomesIgnore = true //deprecated
max_memory = 750.GB
max_cpus = 200
max_time = 24.h
}

80
docs/abims.md Normal file
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@ -0,0 +1,80 @@
# nf-core/configs: ABiMS Configuration
All nf-core pipelines have been successfully configured for use on the ABiMS cluster.
To use, run the pipeline with `-profile abims`. This will download and launch the [`abims.config`](../conf/abims.config) which has been pre-configured with a setup suitable for the ABiMS 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.
## Request an account
You will need an account to use the HPC cluster on ABiMS in order
to run the pipeline. If in doubt see [http://abims.sb-roscoff.fr/account](http://abims.sb-roscoff.fr/account).
## Running the workflow on the ABiMS cluster
Nextflow is installed on the ABiMS cluster.
You need to activate it like this:
```bash
module load nextflow slurm-drmaa graphviz
```
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. Run nextflow from a compute node:
```bash
# Load the dependencies if not done before
module load nextflow slurm-drmaa graphviz
# Run a downloaded/git-cloned nextflow workflow from
srun nextflow run \
/path/to/nf-core/workflow \
-profile abims \
--email my-email@example.org \
-c my-specific.config
...
# Or use let nf-core client download the workflow
srun nextflow run nf-core/rnaseq -profile abims ...
# To launch in background
sbatch --wrap "nextflow run nf-core/rnaseq -profile abims ..."
```
Or write a sbatch script
> nfcore-rnaseq.sh
```bash
#!/bin/bash
#SBATCH -p fast
#SBATCH --mem=4G
module load nextflow slurm-drmaa graphviz
nextflow run nf-core/rnaseq -profile abims ...
```
Launch on the cluster with sbatch:
```bash
sbatch nfcore-rnaseq.sh
```
### Hello, world
nf-core provides some test for each workflow:
```bash
module load nextflow slurm-drmaa graphviz
nextflow run nf-core/rnaseq -profile abims,test
```
## Singularity images mutualized directory
To reduce the disk usage, nf-core images can be stored in a mutualized directory: `/shared/software/singularity/images/nf-core/`
The environment variable `NXF_SINGULARITY_CACHEDIR: /shared/data/cache/nextflow` will indicate this directory to nextflow.
## Databanks
A local copy of several genomes are available in `/shared/bank/` directory.

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@ -10,6 +10,7 @@
//Please use a new line per include Config section to allow easier linting/parsing. Thank you.
profiles {
abims { includeConfig "${params.custom_config_base}/conf/abims.config" }
awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
bi { includeConfig "${params.custom_config_base}/conf/bi.config" }
bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }