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Add documentation about running offline
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@@ -393,3 +393,26 @@ We recommend adding the following line to your environment to limit this (typica | |
```bash | ||
NXF_OPTS='-Xms1g -Xmx4g' | ||
``` | ||
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### Running the pipeline without Internet access | ||
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The pipeline and container images can be downloaded using [nf-core tools](https://nf-co.re/docs/usage/offline). | ||
Here is an example command to download pipeline version 1.1.0 with singularity images: | ||
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``` | ||
nf-core download \ | ||
--container singularity \ | ||
--compress none \ | ||
--revision 1.1.0 \ | ||
raredisease | ||
``` | ||
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Contrary to the paragraph about Nextflow on the nf-core tools page, it is not possible to use the "-all" packaged version of Nextflow. The online version of nextflow is necessary to support the nextflow plugins used for this pipeline. Download instead the file called just `nextflow`. Nextflow will download its dependencies when it is run. Additionally, you need to download the nf-validation plugin explicitly: | ||
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``` | ||
./nextflow plugin install [email protected] | ||
``` | ||
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Now you can transfer the `nextflow` binary as well as its directory `$HOME/.nextflow` to the system without Internet access, and use it there. | ||
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For running offline, you of course have to make all the reference data available locally, and specify `--fasta`, etc., see [above](#reference-files-and-parameters). |