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Replace docker2singularity with singularity native
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docs/getting_started/bids_apps/tutorial.md

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@@ -41,23 +41,17 @@ the docker image will be automatically downloaded from Docker Hub.
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## Running a BIDS App on a cluster (HPC)
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Before a BIDS App can be run on a cluster,
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it first needs to be saved to an Apptainer-compatible image file.1
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This step needs to be performed outside of the cluster (for example on a laptop) and requires Docker:
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HPC clusters typically require Apptainer/Singularity rather than Docker.
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Apptainer (and later versions of Singularity) contain direct support for [Docker/OCI images](https://apptainer.org/docs/user/latest/docker_and_oci.html).
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```bash
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docker run --privileged -ti --rm \
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-v /var/run/docker.sock:/var/run/docker.sock \
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-v /home/srycajal/apptainer_images:/output \
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singularityware/docker2singularity \
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bids/example:0.0.4
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apptainer build bids-example-0.0.7.sif docker://bids/example:0.0.7
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```
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Where `/home/srycajal/apptainer_images` is a path where the image will be stored.
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After transferring the .img file to a cluster it can be run like any other executable:
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```bash
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./bids_example-0.0.4.img /bids_dataset /outputs participant --participant_label 01
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./bids_example-0.0.7.img /bids_dataset /outputs participant --participant_label 01
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```
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## Helpful links

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