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@@ -186,7 +186,8 @@ For FastOMA, we've implemented the following profiles below. Additional ones can
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With `-profile docker` one can use docker as an execution platform. It requires docker to be installed on the system (see [here](https://docs.docker.com/engine/install/)). The pipeline
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will automatically fetch missing containers from dockerhub (e.g. dessimozlab/fastoma) if not found locally. By default, the version
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`latest` is used by the pipeline, however we provide images for any branch and release as well; even for every recent commit.
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One can select the desired container via the `--container_version` argument
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One can select the desired container via the `--container_version` argument. We provide containers for x86_64 (amd64) as well
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as arm64 architectures.
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```
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nextflow run FastOMA.nf -profile docker \
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This will use the container that is tagged with the current commit id. Similarly, one could also use
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`--container_version "0.5.1"` to use the container with version `dessimozlab/fastoma:0.5.1` from dockerhub. Check the latest version on the [DockerHub](https://hub.docker.com/r/dessimozlab/fastoma/tags).
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### Singularity
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### Singularity / Apptainer
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Since Docker needs administrator privileges (root access), [Singluarity](https://apptainer.org/index.html) (a.k.a Apptainer) is a good alternative. This can be installed using [Conda](https://anaconda.org/conda-forge/singularity) with `conda install conda-forge::singularity`. However, in most of the academic HPC cluster, singluarity is already installed and can be called with `module load`.
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With `-profile singularity` singularity containers will be used to run the workflow. It requires singularity to
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be installed on your system. The containers are automatically pulled from dockerhub and converted to singularity
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good overview of what is possible, together with the
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[nextflow documentation on executors](https://www.nextflow.io/docs/latest/executor.html).
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### Large datasets
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Another profile we provide is `-profile large` which is designed for large datasets. It sets much higher limits for the
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maximum amount of memory a process can use (without specifying this profile, jobs will not try to request more than 32 GB
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of RAM).
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All profiles can be combined, e.g. `-profile slurm,conda,large`.
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# How to run FastOMA on the test data
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Note : If you are using FastOMA with Docker or other profiles, check out the difference [here](#using-different-nextflow-profiles).
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### Run on a cluster
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For running on a SLURM cluster, you can add the slurm profile argument: `-profile slurm` to the command line.
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For running on a SLURM cluster, you can add the slurm profile argument: `-profile slurm` to the command line.
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We also recommend to use the singularity/apptainer container, which can be enabled by adding the `singularity` or `apptainer` profile:
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`-profile slurm,singularity` or `-profile slurm,apptainer`.
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