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Merged Jan David Mol requested to merge mol-main-patch-98085 into main
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Prerequisites:
Prerequisites:
* a modern docker (that supports --mount) → this is available on cpu46-50 as part of the "testing" partition, see SDCH-3183 - Verify upgraded Docker on test nodes Work in progres
* a modern docker (that supports --mount) → this is available on cpu46-50 as part of the "testing" partition (see SDCH-3183),
* be able to use docker on the nodes you're going to use (be part of the "docker" group).
* be able to use docker on the nodes you're going to use (be part of the "docker" group),
* run `install_deps.sh` in all nodes that will execute job steps. This will install python3, and the required pip packages.
* run `install_deps.sh` in all nodes that will execute job steps. This will install python3, and the required pip packages.
Then, to run LINC, run `build_and_run.sh`. This will run on CEP4 using cached input in `/data/home/mol`, and output to `/data/tmp/toil/12345/`.
Then, to run LINC, run `build_and_run.sh`. This will run on CEP4 using cached input in `/data/home/mol`, and output to `/data/tmp/toil/12345/`.
 
 
The pipeline runs from the Docker image supplied in this repo, and spawns steps on CEP4 using SLURM (in the "testing" partition). These steps need a bit of toil installed, hence the `install_deps.sh` on each node. For users with a shared homedir, this is not needed as the installation on any node will cause the software to be available on all of them.
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