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remove singularity support

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reasons:

* the kernel running on the compute nodes does not support overlayfs und thus containers downloaded from
  public registries won't run because they lack the /lustre mountpoint

* building containers manually using the Singularity file would work, however nf-core pipelines will stop
  providing these files in future releases
This commit is contained in:
phue 2019-03-12 17:57:31 +00:00
parent 1e2c0c3e04
commit 13df59bfaf
2 changed files with 4 additions and 16 deletions
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2
conf/mendel.config
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@ -11,7 +11,7 @@ manifest {
} }
process { process {
beforeScript = {'module load Singularity; module load Miniconda3'} beforeScript = 'module load Miniconda3/4.6.7'
executor = 'pbspro' executor = 'pbspro'
clusterOptions = { "-P $params.project" } clusterOptions = { "-P $params.project" }
} }

18
docs/mendel.md
View file

@ -2,27 +2,15 @@
All nf-core pipelines have been successfully configured for use on the MENDEL CLUSTER at the Gregor Mendel Institute (GMI). All nf-core pipelines have been successfully configured for use on the MENDEL CLUSTER at the Gregor Mendel Institute (GMI).
To use, run the pipeline with `-profile conda,mendel`. This will download and launch the [`mendel.config`](../conf/mendel.config) which has been pre-configured with a setup suitable for the MENDEL cluster. A Conda environment will be created automatically and software dependencies will be downloaded from ['bioconda'](https://bioconda.github.io/). To use, run the pipeline with `-profile conda,mendel`. This will download and launch the [`mendel.config`](../conf/mendel.config) which has been pre-configured with a setup suitable for the MENDEL cluster. A Conda environment will be created automatically and software dependencies will be resolved via [bioconda](https://bioconda.github.io/).
Theoretically, using `-profile singularity,mendel` would download a docker image containing all of the required software, and convert it to a Singularity image before execution of the pipeline. However, there is a regression in the Singularity deployment on MENDEL which renders containers downloaded from public repositories unusable because they lack the /lustre mountpoint. Before running the pipeline you will need to load Conda using the environment module system on MENDEL. You can do this by issuing the commands below:
If you want to run the pipeline containerized anyway you will have to build the image yourself (on a machine where you have root access) using the provided `Singularity` file in the pipeline repository:
```bash
cd /path/to/pipeline-repository
echo 'mkdir /lustre > Singularity'
singularity build nf-core-methylseq-custom.simg Singularity
```
After you copied the container image to the cluster filesystem, make sure to pass the path to the image to the pipeline with `-with-singularity /path/to/nf-core-methylseq-custom.simg`
Before running the pipeline you will need to load Nextflow and Conda using the environment module system on MENDEL. You can do this by issuing the commands below:
```bash ```bash
## Load Nextflow and Conda environment modules ## Load Nextflow and Conda environment modules
module purge module purge
module load Nextflow module load Nextflow
module load Miniconda3 # not needed if using Singularity module load Miniconda/4.6.7
``` ```
>NB: You will need an account to use the HPC cluster in order to run the pipeline. If in doubt contact the HPC team. >NB: You will need an account to use the HPC cluster in order to run the pipeline. If in doubt contact the HPC team.